tests/testthat/test_splitDataByChromatin.R
In kaiqiong/SOMNiBUS: Smooth modeling of bisulfite sequencing
context("testing splitData by chromatin statess")
source("helper.R", local = TRUE)
# set seed for reproducibility
set.seed(1234)
# create input
positions <- c(41224017:41224026,41224084:41224103,41234773:41234782,
41243842:41243847,41248883:41248888)
my_data <- data.frame(Meth_Counts = sample.int(n = 20, size = length(positions),
replace = TRUE),
Total_Counts = sample.int(n = 70,
size = length(positions),
replace = TRUE),
Position = positions, ID = 1)
my_data <- my_data[order(my_data$Position),]
# require("annotatr")
# annotations = states_annotations(genome = "hg19", "hg19_Hmec-chromatin")
# chr17:41,196,312-41,277,381(GRCh37/hg19 by Entrez Gene)
# Size:81,070 basesOrientation:Minus strand
# r <- GRanges(seqnames = "chr17", ranges = IRanges(start = 41196312, end = 41277381))
# hits <- findOverlaps(query = annotations, subject = r)
# brca_marks <- sort(annotations[queryHits(hits)])
#
# All BRCA1 marks from hg19 genome
# > knitr::kable(as.data.frame(brca_marks))
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:---------------------------------------|:-----|:-------|:------|:----------------------------------|
# |chr17 | 41181674| 41206474| 24801|* |hg19_chromatin_Hmec-WeakTxn:38371 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41206474| 41209474| 3001|* |hg19_chromatin_Hmec-TxnElongation:9428 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41209474| 41213674| 4201|* |hg19_chromatin_Hmec-WeakTxn:38372 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41213674| 41214674| 1001|* |hg19_chromatin_Hmec-TxnElongation:9429 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41214674| 41214874| 201|* |hg19_chromatin_Hmec-WeakTxn:38373 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41214874| 41218874| 4001|* |hg19_chromatin_Hmec-TxnElongation:9430 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41218874| 41220674| 1801|* |hg19_chromatin_Hmec-WeakTxn:38374 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41220674| 41223874| 3201|* |hg19_chromatin_Hmec-TxnElongation:9431 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41223874| 41224274| 401|* |hg19_chromatin_Hmec-WeakTxn:38375 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41224274| 41228074| 3801|* |hg19_chromatin_Hmec-TxnElongation:9432 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41228074| 41231274| 3201|* |hg19_chromatin_Hmec-WeakTxn:38376 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41231274| 41232474| 1201|* |hg19_chromatin_Hmec-TxnElongation:9433 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41232474| 41237274| 4801|* |hg19_chromatin_Hmec-WeakTxn:38377 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41237274| 41248274| 11001|* |hg19_chromatin_Hmec-TxnElongation:9434 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41248274| 41253874| 5601|* |hg19_chromatin_Hmec-WeakTxn:38378 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41253874| 41258274| 4401|* |hg19_chromatin_Hmec-TxnElongation:9435 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41258274| 41271274| 13001|* |hg19_chromatin_Hmec-WeakTxn:38379 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41271274| 41274274| 3001|* |hg19_chromatin_Hmec-TxnElongation:9436 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41274274| 41275674| 1401|* |hg19_chromatin_Hmec-WeakTxn:38380 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41275674| 41275874| 201|* |hg19_chromatin_Hmec-WeakEnhancer:83964 |NA |NA |NA |hg19_chromatin_Hmec-WeakEnhancer |
# |chr17 | 41275874| 41276074| 201|* |hg19_chromatin_Hmec-WeakEnhancer:83965 |NA |NA |NA |hg19_chromatin_Hmec-WeakEnhancer |
# |chr17 | 41276074| 41276274| 201|* |hg19_chromatin_Hmec-WeakPromoter:9953 |NA |NA |NA |hg19_chromatin_Hmec-WeakPromoter |
# |chr17 | 41276274| 41278474| 2201|* |hg19_chromatin_Hmec-ActivePromoter:5485 |NA |NA |NA |hg19_chromatin_Hmec-ActivePromoter |
#
# # Weak transcription BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:---------------------------------|:-----|:-------|:------|:---------------------------|
# |chr17 | 41181674| 41206474| 24801|* |hg19_chromatin_Hmec-WeakTxn:38371 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41209474| 41213674| 4201|* |hg19_chromatin_Hmec-WeakTxn:38372 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41214674| 41214874| 201|* |hg19_chromatin_Hmec-WeakTxn:38373 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41218874| 41220674| 1801|* |hg19_chromatin_Hmec-WeakTxn:38374 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41223874| 41224274| 401|* |hg19_chromatin_Hmec-WeakTxn:38375 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41228074| 41231274| 3201|* |hg19_chromatin_Hmec-WeakTxn:38376 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41232474| 41237274| 4801|* |hg19_chromatin_Hmec-WeakTxn:38377 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41248274| 41253874| 5601|* |hg19_chromatin_Hmec-WeakTxn:38378 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41258274| 41271274| 13001|* |hg19_chromatin_Hmec-WeakTxn:38379 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41274274| 41275674| 1401|* |hg19_chromatin_Hmec-WeakTxn:38380 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
#
# # Weak Elongation BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:--------------------------------------|:-----|:-------|:------|:---------------------------------|
# |chr17 | 41206474| 41209474| 3001|* |hg19_chromatin_Hmec-TxnElongation:9428 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41213674| 41214674| 1001|* |hg19_chromatin_Hmec-TxnElongation:9429 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41214874| 41218874| 4001|* |hg19_chromatin_Hmec-TxnElongation:9430 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41220674| 41223874| 3201|* |hg19_chromatin_Hmec-TxnElongation:9431 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41224274| 41228074| 3801|* |hg19_chromatin_Hmec-TxnElongation:9432 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41231274| 41232474| 1201|* |hg19_chromatin_Hmec-TxnElongation:9433 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41237274| 41248274| 11001|* |hg19_chromatin_Hmec-TxnElongation:9434 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41253874| 41258274| 4401|* |hg19_chromatin_Hmec-TxnElongation:9435 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41271274| 41274274| 3001|* |hg19_chromatin_Hmec-TxnElongation:9436 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
#
# # Weak Enhancer BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:--------------------------------------|:-----|:-------|:------|:--------------------------------|
# |chr17 | 41275674| 41275874| 201|* |hg19_chromatin_Hmec-WeakEnhancer:83964 |NA |NA |NA |hg19_chromatin_Hmec-WeakEnhancer |
# |chr17 | 41275874| 41276074| 201|* |hg19_chromatin_Hmec-WeakEnhancer:83965 |NA |NA |NA |hg19_chromatin_Hmec-WeakEnhancer |
#
#
# # Weak Promoter BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:-------------------------------------|:-----|:-------|:------|:--------------------------------|
# |chr17 | 41276074| 41276274| 201|* |hg19_chromatin_Hmec-WeakPromoter:9953 |NA |NA |NA |hg19_chromatin_Hmec-WeakPromoter |
#
#
# # Strong Promoter BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:---------------------------------------|:-----|:-------|:------|:----------------------------------|
# |chr17 | 41276274| 41278474| 2201|* |hg19_chromatin_Hmec-ActivePromoter:5485 |NA |NA |NA |hg19_chromatin_Hmec-ActivePromoter |
# my_data
# | Meth_Counts| Total_Counts| Position| ID| overlap
# |-----------:|------------:|--------:|--:|
# | 11| 4| 41224017| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 6| 43| 41224018| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 61| 41224019| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 15| 15| 41224020| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 14| 17| 41224021| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 43| 41224022| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 39| 41224023| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 7| 42| 41224024| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 9| 35| 41224025| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 16| 58| 41224026| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 8| 18| 41224084| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 3| 11| 41224085| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 16| 56| 41224086| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 2| 8| 41224087| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 5| 22| 41224088| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 16| 42| 41224089| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 9| 63| 41224090| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 3| 42| 41224091| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 8| 20| 41224092| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 3| 33| 41224093| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 8| 61| 41224094| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 70| 41224095| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 4| 59| 41224096| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 20| 3| 41224097| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 36| 41224098| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 7| 29| 41224099| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 17| 65| 41224100| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 3| 30| 41224101| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 2| 57| 41224102| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 5| 44| 41224103| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 15| 61| 41234773| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 15| 10| 41234774| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 10| 21| 41234775| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 17| 13| 41234776| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 3| 29| 41234777| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 16| 33| 41234778| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 9| 45| 41234779| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 20| 10| 41234780| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 12| 31| 41234781| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 5| 66| 41234782| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 17| 53| 41243842| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 3| 14| 41243843| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 15| 38| 41243844| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 5| 37| 41243845| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 6| 32| 41243846| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 18| 46| 41243847| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 19| 60| 41248883| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 18| 52| 41248884| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 11| 33| 41248885| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 16| 15| 41248886| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 6| 34| 41248887| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 7| 25| 41248888| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
#--test incorrect values--#
test_that(desc = "Test incorrect values",{
expect_error(object = splitDataByChromatin(dat = my_data, chr = "CHR", gap = -1,
min.cpgs = 1, cell.line = "hmec", states = "all", verbose = FALSE),
regexp = "\\'chr\\' should be a character vector which length equals the number of rows in \\'dat\\'.")
expect_error(object = splitDataByChromatin(dat = my_data, chr = NULL, gap = -1,
min.cpgs = 1, cell.line = "hmec", states = "all", verbose = FALSE),
regexp = "\\'chr\\' should be a character vector which length equals the number of rows in \\'dat\\'.")
expect_error(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = 1, cell.line = "hela", states = "all", verbose = FALSE),
regexp = "\\'hela\\' cell line is not supported\\. Choose one among these supported cell lines: \\'gm12878\\', \\'h1hesc\\', \\'hepg2\\', \\'hmec\\', \\'hsmm\\', \\'huvec\\', \\'k562\\', \\'nhek\\', \\'nhlf\\'.")
expect_error(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = 1, cell.line = "hmec", states = "ctcf", verbose = FALSE),
regexp = "None of the requested states are supported\\. Choose among these supported states: \\'all\\', \\'ActivePromoter\\', \\'Heterochrom\\', \\'Insulator\\', \\'PoisedPromoter\\', \\'RepetitiveCNV\\', \\'Repressed\\', \\'StrongEnhancer\\', \\'TxnElongation\\', \\'TxnTransition\\', \\'WeakEnhancer\\', \\'WeakPromoter\\', \\'WeakTxn\\'.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = 1, cell.line = "hmec", states = c("ctcf","ActivePromoter"), verbose = FALSE),
regexp = "The following unsupported states will be ignored: \\'ctcf\\'\\. Choose among these supported states: \\'all\\', \\'ActivePromoter\\', \\'Heterochrom\\', \\'Insulator\\', \\'PoisedPromoter\\', \\'RepetitiveCNV\\', \\'Repressed\\', \\'StrongEnhancer\\', \\'TxnElongation\\', \\'TxnTransition\\', \\'WeakEnhancer\\', \\'WeakPromoter\\', \\'WeakTxn\\'.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = "0",
min.cpgs = 1, cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'gap\\' should be an integer >= -1\\. We will use the default value -1.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -2,
min.cpgs = 1, cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'gap\\' should be an integer >= -1\\. We will use the default value -1.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = "-2", cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'min.cpgs\\' should be a positive integer\\. We will use the default value 50.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = -2, cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'min.cpgs\\' should be a positive integer\\. We will use the default value 50.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
max.cpgs = "-2", cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'max.cpgs\\' should be a positive integer\\. We will use the default value 2000.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
max.cpgs = -2, cell.line = "hmec", states = "ActivePromoter"),
regexp = "\\'max.cpgs\\' should be a positive integer\\. We will use the default value 2000.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = 50, max.cpgs = 2, cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'max.cpgs\\' should be a higher than \\'min.cpgs\\'\\. We will use the default values: min.cpgs=50 and max.cpgs=2000.")
})
test_that("The length of results matches the expected length", {
skip_if_run_bitbucket_pipeline()
#-- min.cpgs = 1, gap = -1, cell.line = "hmec", states = "all" => 4 regions
# ([41224017-41224103],[41234773-41234782],[41243842-41243847],[41248883-41248888])--#
mc_1_intersection_all <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = -1, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = -1, cell.line = "hmec", states = "TxnElongation" => 1 region
# ([41243842-41243847])--#
mc_1_intersection_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = -1, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "all" => 6 regions
# ([41224017-41224103] x 3,[41234773-41234782],[41243842-41248888], [41248883-41248888])--#
mc_1_gap_1kb <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "TxnElongation" => 3 regions
# ([41224017-41224103] x 2,[41243842-41248888] x 1)--#
mc_1_gap_1kb_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "WeakTxn" => 3 regions
# ([41224017-41224103],[41234773-41234782],[41243842-41248888])--#
mc_1_gap_1kb_WeakTxn <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "WeakTxn",
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "ActivePromoter" => 0 region
mc_1_gap_1kb_ActivePromoter <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "ActivePromoter",
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "TxnElongation" => 3 regions
# ([41224017-41224103] x 2,[41243842-41248888] x 1)--#
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "WeakTxn" => 3 regions
# ([41224017-41224103],[41234773-41234782],[41243842-41248888])--#
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "ActivePromoter" => 0 region
# ===> 3 + 3 + 0 = 6
mc_1_gap_1kb_Combined <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = c("WeakTxn","TxnElongation","ActivePromoter"),
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-------#
#-- min.cpgs = 10, gap = -1, cell.line = "hmec", states = "all" => 4 - 2 dropped regions = 2
# ([41224017-41224103],[41234773-41234782])--#
mc_10_intersection_all <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = -1, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = -1, cell.line = "hmec", states = "TxnElongation" => 1 - 1 dropped region = 0
mc_10_intersection_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = -1, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = -1, cell.line = "hmec", states = "WeakTxn" => 3 - 1 dropped region = 2
# ([41224017-41224103],[41234773-41234782])--#
mc_10_intersection_WeakTxn <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "WeakTxn",
gap = -1, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = 1000, cell.line = "hmec", states = "all" => 6 - 1 dropped regions = 5
# ([41224017-41224103] x 3,[41234773-41234782],[41243842-41248888])--#
mc_10_gap_1kb <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = 1000, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = 1000, cell.line = "hmec", states = "TxnElongation" => 3 regions
# ([41224017-41224103] x 2,[41243842-41248888] x 1)--#
mc_10_gap_1kb_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = 1000, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = 1000, cell.line = "hmec", states = "WeakTxn" => 3 - 1 dropped regions = 2
# ([41224017-41224103],[41234773-41234782])--#
mc_10_gap_1kb_WeakTxn <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "WeakTxn",
gap = 1000, min.cpgs = 10, verbose = FALSE)
######
#-- min.cpgs = 10, max.cpgs = 20, gap = -1, cell.line = "hmec", states = "all" => 4 - 3 dropped regions = 1
# ([41234773-41234782])--#
mc_10_max_20_intersection_all <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = -1, min.cpgs = 10, max.cpgs = 20, verbose = FALSE)
#-- min.cpgs = 10, gap = 1000, cell.line = "hmec", states = "all" => 6 - 4 dropped regions = 2
# ([41234773-41234782],[41243842-41248888])--#
mc_10_max_20_gap_1kb <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = 1000, min.cpgs = 10, max.cpgs = 20, verbose = FALSE)
#-- min.cpgs = 5, max.cpgs = 10, gap = 1000, cell.line = "hmec", states = "TxnElongation" => 3 - 3 dropped regions = 0
mc_5_max_10_gap_1kb_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = 1000, min.cpgs = 5, max.cpgs = 10, verbose = FALSE)
expect_true(length(mc_1_intersection_all) == 4)
expect_true(length(mc_1_intersection_TxnElongation) == 1)
expect_true(length(mc_1_gap_1kb) == 6)
expect_true(length(mc_1_gap_1kb_TxnElongation) == 3)
expect_true(length(mc_1_gap_1kb_WeakTxn) == 3)
expect_true(length(mc_1_gap_1kb_ActivePromoter) == 0)
expect_true(length(mc_1_gap_1kb_Combined) == 6)
expect_true(length(mc_10_intersection_all) == 2)
expect_true(length(mc_10_intersection_TxnElongation) == 0)
expect_true(length(mc_10_intersection_WeakTxn) == 2)
expect_true(length(mc_10_gap_1kb) == 5)
expect_true(length(mc_10_gap_1kb_TxnElongation) == 3)
expect_true(length(mc_10_gap_1kb_WeakTxn) == 2)
expect_true(length(mc_10_max_20_intersection_all) == 1)
expect_true(length(mc_10_max_20_gap_1kb) == 2)
expect_true(length(mc_5_max_10_gap_1kb_TxnElongation) == 0)
})
test_that(desc = "Test region dropping",{
skip_if_run_bitbucket_pipeline()
# #--test region dropping--#
m1 <- capture_messages(splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = -1, min.cpgs = 10))
m2 <- capture_messages(splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "WeakTxn",
gap = 1000, min.cpgs = 10))
m3 <- as.character(capture_messages(splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = 1000, min.cpgs = 1, max.cpgs = 20)))
# verbose = FALSE
m4 <- capture_messages(splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = -1, min.cpgs = 10, verbose = FALSE))
expect_match(object = m1[2], regexp = ".*17:41243842-41243847.*6.*10")
expect_match(object = m2[2], regexp = ".*17:41248883-41248888.*6.*10")
expect_match(object = m3[2], regexp = ".*17:41224017-41224103.*30.*20")
expect_true(length(m4) == 0)
})
kaiqiong/SOMNiBUS documentation built on Feb. 24, 2023, 5:38 a.m.
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context("testing splitData by chromatin statess")
source("helper.R", local = TRUE)
# set seed for reproducibility
set.seed(1234)
# create input
positions <- c(41224017:41224026,41224084:41224103,41234773:41234782,
41243842:41243847,41248883:41248888)
my_data <- data.frame(Meth_Counts = sample.int(n = 20, size = length(positions),
replace = TRUE),
Total_Counts = sample.int(n = 70,
size = length(positions),
replace = TRUE),
Position = positions, ID = 1)
my_data <- my_data[order(my_data$Position),]
# require("annotatr")
# annotations = states_annotations(genome = "hg19", "hg19_Hmec-chromatin")
# chr17:41,196,312-41,277,381(GRCh37/hg19 by Entrez Gene)
# Size:81,070 basesOrientation:Minus strand
# r <- GRanges(seqnames = "chr17", ranges = IRanges(start = 41196312, end = 41277381))
# hits <- findOverlaps(query = annotations, subject = r)
# brca_marks <- sort(annotations[queryHits(hits)])
#
# All BRCA1 marks from hg19 genome
# > knitr::kable(as.data.frame(brca_marks))
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:---------------------------------------|:-----|:-------|:------|:----------------------------------|
# |chr17 | 41181674| 41206474| 24801|* |hg19_chromatin_Hmec-WeakTxn:38371 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41206474| 41209474| 3001|* |hg19_chromatin_Hmec-TxnElongation:9428 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41209474| 41213674| 4201|* |hg19_chromatin_Hmec-WeakTxn:38372 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41213674| 41214674| 1001|* |hg19_chromatin_Hmec-TxnElongation:9429 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41214674| 41214874| 201|* |hg19_chromatin_Hmec-WeakTxn:38373 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41214874| 41218874| 4001|* |hg19_chromatin_Hmec-TxnElongation:9430 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41218874| 41220674| 1801|* |hg19_chromatin_Hmec-WeakTxn:38374 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41220674| 41223874| 3201|* |hg19_chromatin_Hmec-TxnElongation:9431 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41223874| 41224274| 401|* |hg19_chromatin_Hmec-WeakTxn:38375 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41224274| 41228074| 3801|* |hg19_chromatin_Hmec-TxnElongation:9432 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41228074| 41231274| 3201|* |hg19_chromatin_Hmec-WeakTxn:38376 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41231274| 41232474| 1201|* |hg19_chromatin_Hmec-TxnElongation:9433 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41232474| 41237274| 4801|* |hg19_chromatin_Hmec-WeakTxn:38377 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41237274| 41248274| 11001|* |hg19_chromatin_Hmec-TxnElongation:9434 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41248274| 41253874| 5601|* |hg19_chromatin_Hmec-WeakTxn:38378 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41253874| 41258274| 4401|* |hg19_chromatin_Hmec-TxnElongation:9435 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41258274| 41271274| 13001|* |hg19_chromatin_Hmec-WeakTxn:38379 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41271274| 41274274| 3001|* |hg19_chromatin_Hmec-TxnElongation:9436 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41274274| 41275674| 1401|* |hg19_chromatin_Hmec-WeakTxn:38380 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41275674| 41275874| 201|* |hg19_chromatin_Hmec-WeakEnhancer:83964 |NA |NA |NA |hg19_chromatin_Hmec-WeakEnhancer |
# |chr17 | 41275874| 41276074| 201|* |hg19_chromatin_Hmec-WeakEnhancer:83965 |NA |NA |NA |hg19_chromatin_Hmec-WeakEnhancer |
# |chr17 | 41276074| 41276274| 201|* |hg19_chromatin_Hmec-WeakPromoter:9953 |NA |NA |NA |hg19_chromatin_Hmec-WeakPromoter |
# |chr17 | 41276274| 41278474| 2201|* |hg19_chromatin_Hmec-ActivePromoter:5485 |NA |NA |NA |hg19_chromatin_Hmec-ActivePromoter |
#
# # Weak transcription BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:---------------------------------|:-----|:-------|:------|:---------------------------|
# |chr17 | 41181674| 41206474| 24801|* |hg19_chromatin_Hmec-WeakTxn:38371 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41209474| 41213674| 4201|* |hg19_chromatin_Hmec-WeakTxn:38372 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41214674| 41214874| 201|* |hg19_chromatin_Hmec-WeakTxn:38373 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41218874| 41220674| 1801|* |hg19_chromatin_Hmec-WeakTxn:38374 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41223874| 41224274| 401|* |hg19_chromatin_Hmec-WeakTxn:38375 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41228074| 41231274| 3201|* |hg19_chromatin_Hmec-WeakTxn:38376 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41232474| 41237274| 4801|* |hg19_chromatin_Hmec-WeakTxn:38377 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41248274| 41253874| 5601|* |hg19_chromatin_Hmec-WeakTxn:38378 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41258274| 41271274| 13001|* |hg19_chromatin_Hmec-WeakTxn:38379 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
# |chr17 | 41274274| 41275674| 1401|* |hg19_chromatin_Hmec-WeakTxn:38380 |NA |NA |NA |hg19_chromatin_Hmec-WeakTxn |
#
# # Weak Elongation BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:--------------------------------------|:-----|:-------|:------|:---------------------------------|
# |chr17 | 41206474| 41209474| 3001|* |hg19_chromatin_Hmec-TxnElongation:9428 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41213674| 41214674| 1001|* |hg19_chromatin_Hmec-TxnElongation:9429 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41214874| 41218874| 4001|* |hg19_chromatin_Hmec-TxnElongation:9430 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41220674| 41223874| 3201|* |hg19_chromatin_Hmec-TxnElongation:9431 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41224274| 41228074| 3801|* |hg19_chromatin_Hmec-TxnElongation:9432 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41231274| 41232474| 1201|* |hg19_chromatin_Hmec-TxnElongation:9433 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41237274| 41248274| 11001|* |hg19_chromatin_Hmec-TxnElongation:9434 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41253874| 41258274| 4401|* |hg19_chromatin_Hmec-TxnElongation:9435 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
# |chr17 | 41271274| 41274274| 3001|* |hg19_chromatin_Hmec-TxnElongation:9436 |NA |NA |NA |hg19_chromatin_Hmec-TxnElongation |
#
# # Weak Enhancer BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:--------------------------------------|:-----|:-------|:------|:--------------------------------|
# |chr17 | 41275674| 41275874| 201|* |hg19_chromatin_Hmec-WeakEnhancer:83964 |NA |NA |NA |hg19_chromatin_Hmec-WeakEnhancer |
# |chr17 | 41275874| 41276074| 201|* |hg19_chromatin_Hmec-WeakEnhancer:83965 |NA |NA |NA |hg19_chromatin_Hmec-WeakEnhancer |
#
#
# # Weak Promoter BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:-------------------------------------|:-----|:-------|:------|:--------------------------------|
# |chr17 | 41276074| 41276274| 201|* |hg19_chromatin_Hmec-WeakPromoter:9953 |NA |NA |NA |hg19_chromatin_Hmec-WeakPromoter |
#
#
# # Strong Promoter BRCA1 marks from hg19 genome
# |seqnames | start| end| width|strand |id |tx_id |gene_id |symbol |type |
# |:--------|--------:|--------:|-----:|:------|:---------------------------------------|:-----|:-------|:------|:----------------------------------|
# |chr17 | 41276274| 41278474| 2201|* |hg19_chromatin_Hmec-ActivePromoter:5485 |NA |NA |NA |hg19_chromatin_Hmec-ActivePromoter |
# my_data
# | Meth_Counts| Total_Counts| Position| ID| overlap
# |-----------:|------------:|--------:|--:|
# | 11| 4| 41224017| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 6| 43| 41224018| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 61| 41224019| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 15| 15| 41224020| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 14| 17| 41224021| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 43| 41224022| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 39| 41224023| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 7| 42| 41224024| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 9| 35| 41224025| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 16| 58| 41224026| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 8| 18| 41224084| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 3| 11| 41224085| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 16| 56| 41224086| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 2| 8| 41224087| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 5| 22| 41224088| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 16| 42| 41224089| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 9| 63| 41224090| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 3| 42| 41224091| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 8| 20| 41224092| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 3| 33| 41224093| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 8| 61| 41224094| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 70| 41224095| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 4| 59| 41224096| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 20| 3| 41224097| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 19| 36| 41224098| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 7| 29| 41224099| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 17| 65| 41224100| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 3| 30| 41224101| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 2| 57| 41224102| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 5| 44| 41224103| 1| gap = -1: WeakTxn:38375; gap = 1000: TxnElongation:9431; WeakTxn:38375; TxnElongation:9432;
# | 15| 61| 41234773| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 15| 10| 41234774| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 10| 21| 41234775| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 17| 13| 41234776| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 3| 29| 41234777| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 16| 33| 41234778| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 9| 45| 41234779| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 20| 10| 41234780| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 12| 31| 41234781| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 5| 66| 41234782| 1| gap = -1: WeakTxn:38377; gap = 1000; WeakTxn:38377;
# | 17| 53| 41243842| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 3| 14| 41243843| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 15| 38| 41243844| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 5| 37| 41243845| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 6| 32| 41243846| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 18| 46| 41243847| 1| gap = -1: TxnElongation:9434; gap = 1000; TxnElongation:9434;
# | 19| 60| 41248883| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 18| 52| 41248884| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 11| 33| 41248885| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 16| 15| 41248886| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 6| 34| 41248887| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
# | 7| 25| 41248888| 1| gap = -1: WeakTxn:38378; gap = 1000; TxnElongation:9434;WeakTxn:38378;
#--test incorrect values--#
test_that(desc = "Test incorrect values",{
expect_error(object = splitDataByChromatin(dat = my_data, chr = "CHR", gap = -1,
min.cpgs = 1, cell.line = "hmec", states = "all", verbose = FALSE),
regexp = "\\'chr\\' should be a character vector which length equals the number of rows in \\'dat\\'.")
expect_error(object = splitDataByChromatin(dat = my_data, chr = NULL, gap = -1,
min.cpgs = 1, cell.line = "hmec", states = "all", verbose = FALSE),
regexp = "\\'chr\\' should be a character vector which length equals the number of rows in \\'dat\\'.")
expect_error(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = 1, cell.line = "hela", states = "all", verbose = FALSE),
regexp = "\\'hela\\' cell line is not supported\\. Choose one among these supported cell lines: \\'gm12878\\', \\'h1hesc\\', \\'hepg2\\', \\'hmec\\', \\'hsmm\\', \\'huvec\\', \\'k562\\', \\'nhek\\', \\'nhlf\\'.")
expect_error(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = 1, cell.line = "hmec", states = "ctcf", verbose = FALSE),
regexp = "None of the requested states are supported\\. Choose among these supported states: \\'all\\', \\'ActivePromoter\\', \\'Heterochrom\\', \\'Insulator\\', \\'PoisedPromoter\\', \\'RepetitiveCNV\\', \\'Repressed\\', \\'StrongEnhancer\\', \\'TxnElongation\\', \\'TxnTransition\\', \\'WeakEnhancer\\', \\'WeakPromoter\\', \\'WeakTxn\\'.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = 1, cell.line = "hmec", states = c("ctcf","ActivePromoter"), verbose = FALSE),
regexp = "The following unsupported states will be ignored: \\'ctcf\\'\\. Choose among these supported states: \\'all\\', \\'ActivePromoter\\', \\'Heterochrom\\', \\'Insulator\\', \\'PoisedPromoter\\', \\'RepetitiveCNV\\', \\'Repressed\\', \\'StrongEnhancer\\', \\'TxnElongation\\', \\'TxnTransition\\', \\'WeakEnhancer\\', \\'WeakPromoter\\', \\'WeakTxn\\'.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = "0",
min.cpgs = 1, cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'gap\\' should be an integer >= -1\\. We will use the default value -1.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -2,
min.cpgs = 1, cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'gap\\' should be an integer >= -1\\. We will use the default value -1.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = "-2", cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'min.cpgs\\' should be a positive integer\\. We will use the default value 50.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = -2, cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'min.cpgs\\' should be a positive integer\\. We will use the default value 50.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
max.cpgs = "-2", cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'max.cpgs\\' should be a positive integer\\. We will use the default value 2000.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
max.cpgs = -2, cell.line = "hmec", states = "ActivePromoter"),
regexp = "\\'max.cpgs\\' should be a positive integer\\. We will use the default value 2000.")
expect_warning(object = splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
min.cpgs = 50, max.cpgs = 2, cell.line = "hmec", states = "ActivePromoter", verbose = FALSE),
regexp = "\\'max.cpgs\\' should be a higher than \\'min.cpgs\\'\\. We will use the default values: min.cpgs=50 and max.cpgs=2000.")
})
test_that("The length of results matches the expected length", {
skip_if_run_bitbucket_pipeline()
#-- min.cpgs = 1, gap = -1, cell.line = "hmec", states = "all" => 4 regions
# ([41224017-41224103],[41234773-41234782],[41243842-41243847],[41248883-41248888])--#
mc_1_intersection_all <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = -1, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = -1, cell.line = "hmec", states = "TxnElongation" => 1 region
# ([41243842-41243847])--#
mc_1_intersection_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = -1, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "all" => 6 regions
# ([41224017-41224103] x 3,[41234773-41234782],[41243842-41248888], [41248883-41248888])--#
mc_1_gap_1kb <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "TxnElongation" => 3 regions
# ([41224017-41224103] x 2,[41243842-41248888] x 1)--#
mc_1_gap_1kb_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "WeakTxn" => 3 regions
# ([41224017-41224103],[41234773-41234782],[41243842-41248888])--#
mc_1_gap_1kb_WeakTxn <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "WeakTxn",
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "ActivePromoter" => 0 region
mc_1_gap_1kb_ActivePromoter <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "ActivePromoter",
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "TxnElongation" => 3 regions
# ([41224017-41224103] x 2,[41243842-41248888] x 1)--#
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "WeakTxn" => 3 regions
# ([41224017-41224103],[41234773-41234782],[41243842-41248888])--#
#-- min.cpgs = 1, gap = 1000, cell.line = "hmec", states = "ActivePromoter" => 0 region
# ===> 3 + 3 + 0 = 6
mc_1_gap_1kb_Combined <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = c("WeakTxn","TxnElongation","ActivePromoter"),
gap = 1000, min.cpgs = 1, verbose = FALSE)
#-------#
#-- min.cpgs = 10, gap = -1, cell.line = "hmec", states = "all" => 4 - 2 dropped regions = 2
# ([41224017-41224103],[41234773-41234782])--#
mc_10_intersection_all <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = -1, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = -1, cell.line = "hmec", states = "TxnElongation" => 1 - 1 dropped region = 0
mc_10_intersection_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = -1, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = -1, cell.line = "hmec", states = "WeakTxn" => 3 - 1 dropped region = 2
# ([41224017-41224103],[41234773-41234782])--#
mc_10_intersection_WeakTxn <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "WeakTxn",
gap = -1, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = 1000, cell.line = "hmec", states = "all" => 6 - 1 dropped regions = 5
# ([41224017-41224103] x 3,[41234773-41234782],[41243842-41248888])--#
mc_10_gap_1kb <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = 1000, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = 1000, cell.line = "hmec", states = "TxnElongation" => 3 regions
# ([41224017-41224103] x 2,[41243842-41248888] x 1)--#
mc_10_gap_1kb_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = 1000, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 10, gap = 1000, cell.line = "hmec", states = "WeakTxn" => 3 - 1 dropped regions = 2
# ([41224017-41224103],[41234773-41234782])--#
mc_10_gap_1kb_WeakTxn <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "WeakTxn",
gap = 1000, min.cpgs = 10, verbose = FALSE)
######
#-- min.cpgs = 10, max.cpgs = 20, gap = -1, cell.line = "hmec", states = "all" => 4 - 3 dropped regions = 1
# ([41234773-41234782])--#
mc_10_max_20_intersection_all <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = -1, min.cpgs = 10, max.cpgs = 20, verbose = FALSE)
#-- min.cpgs = 10, gap = 1000, cell.line = "hmec", states = "all" => 6 - 4 dropped regions = 2
# ([41234773-41234782],[41243842-41248888])--#
mc_10_max_20_gap_1kb <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = 1000, min.cpgs = 10, max.cpgs = 20, verbose = FALSE)
#-- min.cpgs = 5, max.cpgs = 10, gap = 1000, cell.line = "hmec", states = "TxnElongation" => 3 - 3 dropped regions = 0
mc_5_max_10_gap_1kb_TxnElongation <- splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = 1000, min.cpgs = 5, max.cpgs = 10, verbose = FALSE)
expect_true(length(mc_1_intersection_all) == 4)
expect_true(length(mc_1_intersection_TxnElongation) == 1)
expect_true(length(mc_1_gap_1kb) == 6)
expect_true(length(mc_1_gap_1kb_TxnElongation) == 3)
expect_true(length(mc_1_gap_1kb_WeakTxn) == 3)
expect_true(length(mc_1_gap_1kb_ActivePromoter) == 0)
expect_true(length(mc_1_gap_1kb_Combined) == 6)
expect_true(length(mc_10_intersection_all) == 2)
expect_true(length(mc_10_intersection_TxnElongation) == 0)
expect_true(length(mc_10_intersection_WeakTxn) == 2)
expect_true(length(mc_10_gap_1kb) == 5)
expect_true(length(mc_10_gap_1kb_TxnElongation) == 3)
expect_true(length(mc_10_gap_1kb_WeakTxn) == 2)
expect_true(length(mc_10_max_20_intersection_all) == 1)
expect_true(length(mc_10_max_20_gap_1kb) == 2)
expect_true(length(mc_5_max_10_gap_1kb_TxnElongation) == 0)
})
test_that(desc = "Test region dropping",{
skip_if_run_bitbucket_pipeline()
# #--test region dropping--#
m1 <- capture_messages(splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = -1, min.cpgs = 10))
m2 <- capture_messages(splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "WeakTxn",
gap = 1000, min.cpgs = 10))
m3 <- as.character(capture_messages(splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "all",
gap = 1000, min.cpgs = 1, max.cpgs = 20)))
# verbose = FALSE
m4 <- capture_messages(splitDataByChromatin(dat = my_data, chr = rep("chr17", nrow(my_data)),
cell.line = "hmec", states = "TxnElongation",
gap = -1, min.cpgs = 10, verbose = FALSE))
expect_match(object = m1[2], regexp = ".*17:41243842-41243847.*6.*10")
expect_match(object = m2[2], regexp = ".*17:41248883-41248888.*6.*10")
expect_match(object = m3[2], regexp = ".*17:41224017-41224103.*30.*20")
expect_true(length(m4) == 0)
})
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