tests/testthat/test_splitDataByGene.R
In kaiqiong/SOMNiBUS: Smooth modeling of bisulfite sequencing
context("testing splitData by genomic regions")
source("helper.R", local = TRUE)
# set seed for reproducibility
set.seed(1234)
# create input
positions <- c(43072000:43072009,43072067:43072086,43082756:43082765,
43091825:43091830,43096866:43096871)
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$Position),]
# require("annotatr")
# annotations = build_annotations(genome = "hg38",
# annotations = "hg38_genes_promoters")
# prom <- sort(annotations[!is.na(annotations$symbol) &
# annotations$symbol == "BRCA1"])[1:5]
#
# BRCA1 promoters from hg38 genome
# GAP = -1 (intersection)
# seqnames ranges strand | id tx_id gene_id symbol type
# <Rle> <IRanges> <Rle> | <character> <character> <character> <character> <character>
# chr17 43071067-43072066 - | promoter:184718 ENST00000472490.1 672 BRCA1 hg38_genes_promoters
# chr17 43082761-43083760 - | promoter:184719 ENST00000621897.1 672 BRCA1 hg38_genes_promoters
# chr17 43091825-43092824 - | promoter:184721 ENST00000461574.1 672 BRCA1 hg38_genes_promoters
# chr17 43091852-43092851 - | promoter:184708 ENST00000644379.1 672 BRCA1 hg38_genes_promoters
# chr17 43095867-43096866 - | promoter:184724 ENST00000412061.3 672 BRCA1 hg38_genes_promoters
#
#
# GAP = 0 (adjacent)
# seqnames ranges strand | id tx_id gene_id symbol type
# <Rle> <IRanges> <Rle> | <character> <character> <character> <character> <character>
# chr17 43071066-43072067 - | promoter:184718 ENST00000472490.1 672 BRCA1 hg38_genes_promoters
# chr17 43082760-43083761 - | promoter:184719 ENST00000621897.1 672 BRCA1 hg38_genes_promoters
# chr17 43091824-43092825 - | promoter:184721 ENST00000461574.1 672 BRCA1 hg38_genes_promoters
# chr17 43091851-43092852 - | promoter:184708 ENST00000644379.1 672 BRCA1 hg38_genes_promoters
# chr17 43095866-43096867 - | promoter:184724 ENST00000412061.3 672 BRCA1 hg38_genes_promoters
#
#
# GAP = 5
# seqnames ranges strand | id tx_id gene_id symbol type
# <Rle> <IRanges> <Rle> | <character> <character> <character> <character> <character>
# chr17 43071062-43072071 - | promoter:184718 ENST00000472490.1 672 BRCA1 hg38_genes_promoters
# chr17 43082756-43083765 - | promoter:184719 ENST00000621897.1 672 BRCA1 hg38_genes_promoters
# chr17 43091820-43092829 - | promoter:184721 ENST00000461574.1 672 BRCA1 hg38_genes_promoters
# chr17 43091847-43092856 - | promoter:184708 ENST00000644379.1 672 BRCA1 hg38_genes_promoters
# chr17 43095862-43096871 - | promoter:184724 ENST00000412061.3 672 BRCA1 hg38_genes_promoters
# my_data
# | Meth_Counts| Total_Counts|Chrom | Position| ID| overlap
# |-----------:|------------:|:-----|--------:|--:|
# | 15| 8|17 | 43072000| 1|gap = -1 [promoter:184718]
# | 4| 21|17 | 43072001| 1|gap = -1 [promoter:184718]
# | 13| 34|17 | 43072002| 1|gap = -1 [promoter:184718]
# | 12| 21|17 | 43072003| 1|gap = -1 [promoter:184718]
# | 10| 64|17 | 43072004| 1|gap = -1 [promoter:184718]
# | 12| 39|17 | 43072005| 1|gap = -1 [promoter:184718]
# | 10| 39|17 | 43072006| 1|gap = -1 [promoter:184718]
# | 17| 19|17 | 43072007| 1|gap = -1 [promoter:184718]
# | 17| 45|17 | 43072008| 1|gap = -1 [promoter:184718]
# | 6| 30|17 | 43072009| 1|gap = -1 [promoter:184718]
# | 11| 66|17 | 43072067| 1|gap = 0 [promoter:184718]
# | 6| 61|17 | 43072068| 1|gap = 5 [promoter:184718]
# | 8| 22|17 | 43072069| 1|gap = 5 [promoter:184718]
# | 19| 46|17 | 43072070| 1|gap = 5 [promoter:184718]
# | 15| 65|17 | 43072071| 1|gap = 5 [promoter:184718]
# | 3| 25|17 | 43072072| 1|gap = 5 [promoter:184718]
# | 2| 27|17 | 43072073| 1|
# | 13| 11|17 | 43072074| 1|
# | 10| 69|17 | 43072075| 1|
# | 13| 2|17 | 43072076| 1|
# | 7| 27|17 | 43072077| 1|
# | 14| 44|17 | 43072078| 1|
# | 17| 17|17 | 43072079| 1|
# | 17| 1|17 | 43072080| 1|
# | 20| 70|17 | 43072081| 1|
# | 8| 28|17 | 43072082| 1|
# | 1| 20|17 | 43072083| 1|
# | 9| 68|17 | 43072084| 1|
# | 17| 65|17 | 43072085| 1|
# | 14| 14|17 | 43072086| 1|
#
# | 10| 3|17 | 43082756| 1|gap = 5 [promoter:184719]
# | 19| 68|17 | 43082757| 1|gap = 5 [promoter:184719]
# | 16| 37|17 | 43082758| 1|gap = 5 [promoter:184719]
# | 2| 17|17 | 43082759| 1|gap = 5 [promoter:184719]
# | 11| 40|17 | 43082760| 1|gap = 0 [promoter:184719]
# | 20| 25|17 | 43082761| 1|gap = -1 [promoter:184719]
# | 11| 43|17 | 43082762| 1|gap = -1 [promoter:184719]
# | 16| 65|17 | 43082763| 1|gap = -1 [promoter:184719]
# | 15| 31|17 | 43082764| 1|gap = -1 [promoter:184719]
# | 6| 18|17 | 43082765| 1|gap = -1 [promoter:184719]
#
# | 10| 24|17 | 43091825| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 7| 66|17 | 43091826| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 6| 29|17 | 43091827| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 17| 38|17 | 43091828| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 4| 7|17 | 43091829| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 15| 2|17 | 43091830| 1|gap = -1 [promoter:184721] [3UTR:125803]
#
# | 19| 60|17 | 43096866| 1|gap = -1 [promoter:184724]
# | 18| 52|17 | 43096867| 1|gap = 0 [promoter:184724]
# | 11| 33|17 | 43096868| 1|gap = 5 [promoter:184724]
# | 16| 15|17 | 43096869| 1|gap = 5 [promoter:184724]
# | 6| 34|17 | 43096870| 1|gap = 5 [promoter:184724]
# | 7| 25|17 | 43096871| 1|gap = 5 [promoter:184724]
#--test incorrect values--#
test_that(desc = "Test incorrect values",{
expect_error(object = splitDataByGene(dat = my_data, chr = "CHR", gap = -1,
types = "exon", min.cpgs = 1, organism = "human", build = "hg19", verbose = FALSE),
regexp = "\\'chr\\' should be a character vector which length equals the number of rows in \\'dat\\'.")
expect_error(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = 1, organism = "lupus", build = "hg19", verbose = FALSE),
regexp = "\\'lupus\\' organism is not supported\\. Choose one among these supported types: \\'human\\', \\'mouse\\', \\'rat\\', \\'fly\\'.")
expect_error(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = 1, organism = "human", build = "hg18", verbose = FALSE),
regexp = "\\'hg18\\' build is not supported\\. Choose one among these supported builds: \\'hg38\\', \\'hg19\\'.")
expect_error(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = 1, organism = "mouse", build = "mm10", verbose = FALSE),
regexp = "Please install the following package\\(s\\) in order to perform the requested partiniong: \\'TxDb.Mmusculus.UCSC.mm10.knownGene\\', \\'org.Mm.eg.db\\'.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = "0",
types = "exon", min.cpgs = 1, organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'gap\\' should be an integer >= -1\\. We will use the default value -1.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -2,
types = "exon", min.cpgs = 1, organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'gap\\' should be an integer >= -1\\. We will use the default value -1.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = "-2", organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'min.cpgs\\' should be a positive integer\\. We will use the default value 50.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = -2, organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'min.cpgs\\' should be a positive integer\\. We will use the default value 50.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", max.cpgs = "-2", organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'max.cpgs\\' should be a positive integer\\. We will use the default value 2000.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", max.cpgs = -2, organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'max.cpgs\\' should be a positive integer\\. We will use the default value 2000.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = 50, max.cpgs = 2, organism = "human", build = "hg38", 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.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = c("promoter", "coding"), min.cpgs = 2, organism = "human", build = "hg19", verbose = FALSE),
regexp = "The following unsupported types will be ignored: \\'coding\\'\\. Choose among these supported types: \\'all\\', \\'upstream\\', \\'threeprime\\', \\'fiveprime\\', \\'promoter\\', \\'exon\\', \\'intron\\'.")
expect_error(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "coding", min.cpgs = 2, organism = "human", build = "hg19", verbose = FALSE),
regexp = "None of the requested types are supported\\. Choose among these supported types: \\'all\\', \\'upstream\\', \\'threeprime\\', \\'fiveprime\\', \\'promoter\\', \\'exon\\', \\'intron\\'.")
})
test_that("The length of results matches the expected length", {
skip_if_run_bitbucket_pipeline()
#-- min.cpgs = 1, gap = -1, organism = "human", build = "hg38" => 4 regions
# ([43072000-43072009],[43082761-43082765],[43091825-43091830],[43096866])--#
mc_1_intersection <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = -1, organism = "human", build = "hg38" => 4 regions
# promoter: ([43072000-43072009],[43082761-43082765],[43091825-43091830],[43096866])--#
# threeprime: [43091825-43091830]
mc_1_combined <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = c("promoter","threeprime"), gap = -1, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 0, organism = "human", build = "hg38" => 4 regions
# ([43072000-43072067],[43082760-43082765],[43091825-43091830], [43096866-43096867])--#
mc_1_gap_adjacent <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 0, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 5, organism = "human", build = "hg38" => 4 regions
# ([43072000-43072072],[43082756-43082765],[43091825-43091830], [43096866-43096871])--#
mc_1_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 5, gap = -1, organism = "human", build = "hg38" => 3 regions (4 - 1 drop)
# ([43072000-43072009],[43082761-43082765],[43091825-43091830])--#
mc_5_intersection <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 5, verbose = FALSE)
#-- min.cpgs = 5, gap = 0, organism = "human", build = "hg38" => 3 regions (4 - 1 drop)
# ([43072000-43072067],[43082760-43082765],[43091825-43091830])--#
mc_5_gap_adjacent <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 0, min.cpgs = 5, verbose = FALSE)
#-- min.cpgs = 1, gap = 5, organism = "human", build = "hg38" => 4 regions
# ([43072000-43072072],[43082756-43082765],[43091825-43091830], [43096866-43096871])--#
mc_5_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5, min.cpgs = 5, verbose = FALSE)
#-- min.cpgs = 10, gap = -1, organism = "human", build = "hg38" => 1 region (4 - 3 drop)
# ([43072000-43072009])--#
mc_10_intersection <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 5, gap = 0, organism = "human", build = "hg38" => 1 region (4 - 3 drop)
# ([43072000-43072067])--#
mc_10_gap_adjacent <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 0, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 1, gap = 5, organism = "human", build = "hg38" => 2 regions (4 - 2 drop)
# ([43072000-43072072],[43082756-43082765])--#
mc_10_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 5, max.cpgs = 10, gap = 5, organism = "human", build = "hg38" => 3 regions + 1 drop [43072000-43072072]
# ([43082756-43082765],[43091825-43091830], [43096866-43096871])--#
mc_5_max_10_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5,
min.cpgs = 5, max.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 1, max.cpgs = 10, gap = -1, organism = "human", build = "hg38" => 4 regions
mc_1_max_10_intersection <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 1,
max.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 1, gap = 5, organism = "human", build = "hg38" => 1 regions (4 - 3 drop)
# ([43082756-43082765])--#
mc_10_max_15_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5, min.cpgs = 10,
max.cpgs = 15, verbose = FALSE)
expect_true(length(mc_1_intersection) == 4)
expect_true(length(mc_1_combined) == 5)
expect_true(length(mc_1_gap_adjacent) == 4)
expect_true(length(mc_1_gap_5) == 4)
expect_true(length(mc_5_intersection) == 3)
expect_true(length(mc_5_gap_adjacent) == 3)
expect_true(length(mc_5_gap_5) == 4)
expect_true(length(mc_10_intersection) == 1)
expect_true(length(mc_10_gap_adjacent) == 1)
expect_true(length(mc_10_gap_5) == 2)
expect_true(length(mc_5_max_10_gap_5) == 3)
expect_true(length(mc_1_max_10_intersection) == 4)
expect_true(length(mc_10_max_15_gap_5) == 1)
})
test_that(desc = "Test region dropping",{
skip_if_run_bitbucket_pipeline()
# #--test region dropping--#
m1 <- capture_messages(splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 5))
m2 <- capture_messages(splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 0, min.cpgs = 5))
m3 <- capture_messages(splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5,
min.cpgs = 5, max.cpgs = 10))
m4 <- capture_messages(splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5,
min.cpgs = 5, max.cpgs = 10,
verbose = FALSE))
expect_match(object = m1[2], regexp = ".*17:43096866.*1.*5")
expect_match(object = m2[2], regexp = ".*17:43096866-43096867.*2.*5")
expect_match(object = m3[2], regexp = ".*17:43072000-43072072.*16.*10")
expect_true(length(m4) == 0)
})
kaiqiong/SOMNiBUS documentation built on Feb. 24, 2023, 5:38 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
context("testing splitData by genomic regions")
source("helper.R", local = TRUE)
# set seed for reproducibility
set.seed(1234)
# create input
positions <- c(43072000:43072009,43072067:43072086,43082756:43082765,
43091825:43091830,43096866:43096871)
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 = build_annotations(genome = "hg38",
# annotations = "hg38_genes_promoters")
# prom <- sort(annotations[!is.na(annotations$symbol) &
# annotations$symbol == "BRCA1"])[1:5]
#
# BRCA1 promoters from hg38 genome
# GAP = -1 (intersection)
# seqnames ranges strand | id tx_id gene_id symbol type
# <Rle> <IRanges> <Rle> | <character> <character> <character> <character> <character>
# chr17 43071067-43072066 - | promoter:184718 ENST00000472490.1 672 BRCA1 hg38_genes_promoters
# chr17 43082761-43083760 - | promoter:184719 ENST00000621897.1 672 BRCA1 hg38_genes_promoters
# chr17 43091825-43092824 - | promoter:184721 ENST00000461574.1 672 BRCA1 hg38_genes_promoters
# chr17 43091852-43092851 - | promoter:184708 ENST00000644379.1 672 BRCA1 hg38_genes_promoters
# chr17 43095867-43096866 - | promoter:184724 ENST00000412061.3 672 BRCA1 hg38_genes_promoters
#
#
# GAP = 0 (adjacent)
# seqnames ranges strand | id tx_id gene_id symbol type
# <Rle> <IRanges> <Rle> | <character> <character> <character> <character> <character>
# chr17 43071066-43072067 - | promoter:184718 ENST00000472490.1 672 BRCA1 hg38_genes_promoters
# chr17 43082760-43083761 - | promoter:184719 ENST00000621897.1 672 BRCA1 hg38_genes_promoters
# chr17 43091824-43092825 - | promoter:184721 ENST00000461574.1 672 BRCA1 hg38_genes_promoters
# chr17 43091851-43092852 - | promoter:184708 ENST00000644379.1 672 BRCA1 hg38_genes_promoters
# chr17 43095866-43096867 - | promoter:184724 ENST00000412061.3 672 BRCA1 hg38_genes_promoters
#
#
# GAP = 5
# seqnames ranges strand | id tx_id gene_id symbol type
# <Rle> <IRanges> <Rle> | <character> <character> <character> <character> <character>
# chr17 43071062-43072071 - | promoter:184718 ENST00000472490.1 672 BRCA1 hg38_genes_promoters
# chr17 43082756-43083765 - | promoter:184719 ENST00000621897.1 672 BRCA1 hg38_genes_promoters
# chr17 43091820-43092829 - | promoter:184721 ENST00000461574.1 672 BRCA1 hg38_genes_promoters
# chr17 43091847-43092856 - | promoter:184708 ENST00000644379.1 672 BRCA1 hg38_genes_promoters
# chr17 43095862-43096871 - | promoter:184724 ENST00000412061.3 672 BRCA1 hg38_genes_promoters
# my_data
# | Meth_Counts| Total_Counts|Chrom | Position| ID| overlap
# |-----------:|------------:|:-----|--------:|--:|
# | 15| 8|17 | 43072000| 1|gap = -1 [promoter:184718]
# | 4| 21|17 | 43072001| 1|gap = -1 [promoter:184718]
# | 13| 34|17 | 43072002| 1|gap = -1 [promoter:184718]
# | 12| 21|17 | 43072003| 1|gap = -1 [promoter:184718]
# | 10| 64|17 | 43072004| 1|gap = -1 [promoter:184718]
# | 12| 39|17 | 43072005| 1|gap = -1 [promoter:184718]
# | 10| 39|17 | 43072006| 1|gap = -1 [promoter:184718]
# | 17| 19|17 | 43072007| 1|gap = -1 [promoter:184718]
# | 17| 45|17 | 43072008| 1|gap = -1 [promoter:184718]
# | 6| 30|17 | 43072009| 1|gap = -1 [promoter:184718]
# | 11| 66|17 | 43072067| 1|gap = 0 [promoter:184718]
# | 6| 61|17 | 43072068| 1|gap = 5 [promoter:184718]
# | 8| 22|17 | 43072069| 1|gap = 5 [promoter:184718]
# | 19| 46|17 | 43072070| 1|gap = 5 [promoter:184718]
# | 15| 65|17 | 43072071| 1|gap = 5 [promoter:184718]
# | 3| 25|17 | 43072072| 1|gap = 5 [promoter:184718]
# | 2| 27|17 | 43072073| 1|
# | 13| 11|17 | 43072074| 1|
# | 10| 69|17 | 43072075| 1|
# | 13| 2|17 | 43072076| 1|
# | 7| 27|17 | 43072077| 1|
# | 14| 44|17 | 43072078| 1|
# | 17| 17|17 | 43072079| 1|
# | 17| 1|17 | 43072080| 1|
# | 20| 70|17 | 43072081| 1|
# | 8| 28|17 | 43072082| 1|
# | 1| 20|17 | 43072083| 1|
# | 9| 68|17 | 43072084| 1|
# | 17| 65|17 | 43072085| 1|
# | 14| 14|17 | 43072086| 1|
#
# | 10| 3|17 | 43082756| 1|gap = 5 [promoter:184719]
# | 19| 68|17 | 43082757| 1|gap = 5 [promoter:184719]
# | 16| 37|17 | 43082758| 1|gap = 5 [promoter:184719]
# | 2| 17|17 | 43082759| 1|gap = 5 [promoter:184719]
# | 11| 40|17 | 43082760| 1|gap = 0 [promoter:184719]
# | 20| 25|17 | 43082761| 1|gap = -1 [promoter:184719]
# | 11| 43|17 | 43082762| 1|gap = -1 [promoter:184719]
# | 16| 65|17 | 43082763| 1|gap = -1 [promoter:184719]
# | 15| 31|17 | 43082764| 1|gap = -1 [promoter:184719]
# | 6| 18|17 | 43082765| 1|gap = -1 [promoter:184719]
#
# | 10| 24|17 | 43091825| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 7| 66|17 | 43091826| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 6| 29|17 | 43091827| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 17| 38|17 | 43091828| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 4| 7|17 | 43091829| 1|gap = -1 [promoter:184721] [3UTR:125803]
# | 15| 2|17 | 43091830| 1|gap = -1 [promoter:184721] [3UTR:125803]
#
# | 19| 60|17 | 43096866| 1|gap = -1 [promoter:184724]
# | 18| 52|17 | 43096867| 1|gap = 0 [promoter:184724]
# | 11| 33|17 | 43096868| 1|gap = 5 [promoter:184724]
# | 16| 15|17 | 43096869| 1|gap = 5 [promoter:184724]
# | 6| 34|17 | 43096870| 1|gap = 5 [promoter:184724]
# | 7| 25|17 | 43096871| 1|gap = 5 [promoter:184724]
#--test incorrect values--#
test_that(desc = "Test incorrect values",{
expect_error(object = splitDataByGene(dat = my_data, chr = "CHR", gap = -1,
types = "exon", min.cpgs = 1, organism = "human", build = "hg19", verbose = FALSE),
regexp = "\\'chr\\' should be a character vector which length equals the number of rows in \\'dat\\'.")
expect_error(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = 1, organism = "lupus", build = "hg19", verbose = FALSE),
regexp = "\\'lupus\\' organism is not supported\\. Choose one among these supported types: \\'human\\', \\'mouse\\', \\'rat\\', \\'fly\\'.")
expect_error(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = 1, organism = "human", build = "hg18", verbose = FALSE),
regexp = "\\'hg18\\' build is not supported\\. Choose one among these supported builds: \\'hg38\\', \\'hg19\\'.")
expect_error(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = 1, organism = "mouse", build = "mm10", verbose = FALSE),
regexp = "Please install the following package\\(s\\) in order to perform the requested partiniong: \\'TxDb.Mmusculus.UCSC.mm10.knownGene\\', \\'org.Mm.eg.db\\'.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = "0",
types = "exon", min.cpgs = 1, organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'gap\\' should be an integer >= -1\\. We will use the default value -1.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -2,
types = "exon", min.cpgs = 1, organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'gap\\' should be an integer >= -1\\. We will use the default value -1.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = "-2", organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'min.cpgs\\' should be a positive integer\\. We will use the default value 50.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = -2, organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'min.cpgs\\' should be a positive integer\\. We will use the default value 50.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", max.cpgs = "-2", organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'max.cpgs\\' should be a positive integer\\. We will use the default value 2000.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", max.cpgs = -2, organism = "human", build = "hg38", verbose = FALSE),
regexp = "\\'max.cpgs\\' should be a positive integer\\. We will use the default value 2000.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "exon", min.cpgs = 50, max.cpgs = 2, organism = "human", build = "hg38", 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.")
expect_warning(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = c("promoter", "coding"), min.cpgs = 2, organism = "human", build = "hg19", verbose = FALSE),
regexp = "The following unsupported types will be ignored: \\'coding\\'\\. Choose among these supported types: \\'all\\', \\'upstream\\', \\'threeprime\\', \\'fiveprime\\', \\'promoter\\', \\'exon\\', \\'intron\\'.")
expect_error(object = splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)), gap = -1,
types = "coding", min.cpgs = 2, organism = "human", build = "hg19", verbose = FALSE),
regexp = "None of the requested types are supported\\. Choose among these supported types: \\'all\\', \\'upstream\\', \\'threeprime\\', \\'fiveprime\\', \\'promoter\\', \\'exon\\', \\'intron\\'.")
})
test_that("The length of results matches the expected length", {
skip_if_run_bitbucket_pipeline()
#-- min.cpgs = 1, gap = -1, organism = "human", build = "hg38" => 4 regions
# ([43072000-43072009],[43082761-43082765],[43091825-43091830],[43096866])--#
mc_1_intersection <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = -1, organism = "human", build = "hg38" => 4 regions
# promoter: ([43072000-43072009],[43082761-43082765],[43091825-43091830],[43096866])--#
# threeprime: [43091825-43091830]
mc_1_combined <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = c("promoter","threeprime"), gap = -1, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 0, organism = "human", build = "hg38" => 4 regions
# ([43072000-43072067],[43082760-43082765],[43091825-43091830], [43096866-43096867])--#
mc_1_gap_adjacent <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 0, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 1, gap = 5, organism = "human", build = "hg38" => 4 regions
# ([43072000-43072072],[43082756-43082765],[43091825-43091830], [43096866-43096871])--#
mc_1_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5, min.cpgs = 1, verbose = FALSE)
#-- min.cpgs = 5, gap = -1, organism = "human", build = "hg38" => 3 regions (4 - 1 drop)
# ([43072000-43072009],[43082761-43082765],[43091825-43091830])--#
mc_5_intersection <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 5, verbose = FALSE)
#-- min.cpgs = 5, gap = 0, organism = "human", build = "hg38" => 3 regions (4 - 1 drop)
# ([43072000-43072067],[43082760-43082765],[43091825-43091830])--#
mc_5_gap_adjacent <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 0, min.cpgs = 5, verbose = FALSE)
#-- min.cpgs = 1, gap = 5, organism = "human", build = "hg38" => 4 regions
# ([43072000-43072072],[43082756-43082765],[43091825-43091830], [43096866-43096871])--#
mc_5_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5, min.cpgs = 5, verbose = FALSE)
#-- min.cpgs = 10, gap = -1, organism = "human", build = "hg38" => 1 region (4 - 3 drop)
# ([43072000-43072009])--#
mc_10_intersection <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 5, gap = 0, organism = "human", build = "hg38" => 1 region (4 - 3 drop)
# ([43072000-43072067])--#
mc_10_gap_adjacent <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 0, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 1, gap = 5, organism = "human", build = "hg38" => 2 regions (4 - 2 drop)
# ([43072000-43072072],[43082756-43082765])--#
mc_10_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5, min.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 5, max.cpgs = 10, gap = 5, organism = "human", build = "hg38" => 3 regions + 1 drop [43072000-43072072]
# ([43082756-43082765],[43091825-43091830], [43096866-43096871])--#
mc_5_max_10_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5,
min.cpgs = 5, max.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 1, max.cpgs = 10, gap = -1, organism = "human", build = "hg38" => 4 regions
mc_1_max_10_intersection <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 1,
max.cpgs = 10, verbose = FALSE)
#-- min.cpgs = 1, gap = 5, organism = "human", build = "hg38" => 1 regions (4 - 3 drop)
# ([43082756-43082765])--#
mc_10_max_15_gap_5 <- splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5, min.cpgs = 10,
max.cpgs = 15, verbose = FALSE)
expect_true(length(mc_1_intersection) == 4)
expect_true(length(mc_1_combined) == 5)
expect_true(length(mc_1_gap_adjacent) == 4)
expect_true(length(mc_1_gap_5) == 4)
expect_true(length(mc_5_intersection) == 3)
expect_true(length(mc_5_gap_adjacent) == 3)
expect_true(length(mc_5_gap_5) == 4)
expect_true(length(mc_10_intersection) == 1)
expect_true(length(mc_10_gap_adjacent) == 1)
expect_true(length(mc_10_gap_5) == 2)
expect_true(length(mc_5_max_10_gap_5) == 3)
expect_true(length(mc_1_max_10_intersection) == 4)
expect_true(length(mc_10_max_15_gap_5) == 1)
})
test_that(desc = "Test region dropping",{
skip_if_run_bitbucket_pipeline()
# #--test region dropping--#
m1 <- capture_messages(splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = -1, min.cpgs = 5))
m2 <- capture_messages(splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 0, min.cpgs = 5))
m3 <- capture_messages(splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5,
min.cpgs = 5, max.cpgs = 10))
m4 <- capture_messages(splitDataByGene(dat = my_data, chr = rep("chr17", nrow(my_data)),
organism = "human", build = "hg38",
types = "promoter", gap = 5,
min.cpgs = 5, max.cpgs = 10,
verbose = FALSE))
expect_match(object = m1[2], regexp = ".*17:43096866.*1.*5")
expect_match(object = m2[2], regexp = ".*17:43096866-43096867.*2.*5")
expect_match(object = m3[2], regexp = ".*17:43072000-43072072.*16.*10")
expect_true(length(m4) == 0)
})
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.