R/Import_Filter.R
In bmansfeld/QTLseqR: QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.
Defines functions
importFromGATK
importFromTable
importFromVCF
Documented in
importFromGATK
importFromTable
#' Imports SNP data from GATK VariablesToTable output
#'
#' Imports SNP data from the output of the
#' \href{https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_VariantsToTable.php}{VariantsToTable}
#' function in GATK. After importing the data, the function then calculates
#' total reference allele frequency for both bulks together, the delta SNP index
#' (i.e. SNP index of the low bulk subtracted from the SNP index of the high
#' bulk), the G statistic and returns a data frame. The required GATK fields
#' (-F) are CHROM (Chromosome) and POS (Position). The required Genotype fields
#' (-GF) are AD (Allele Depth), DP (Depth). Recommended
#' fields are REF (Reference allele) and ALT (Alternative allele) Recommended
#' Genotype feilds are PL (Phred-scaled likelihoods) and GQ (Genotype Quality).
#'
#' @param file The name of the GATK VariablesToTable output .table file which the
#' data are to be read from.
#' @param highBulk The sample name of the High Bulk
#' @param lowBulk The sample name of the Low Bulk
#' @param chromList a string vector of the chromosomes to be used in the
#' analysis. Useful for filtering out unwanted contigs etc.
#' @return Returns a data frame containing columns for Read depth (DP),
#' Reference Allele Depth (AD_REF) and Alternative Allele Depth (AD_ALT),
#' Genoytype Quality (GQ) and SNPindex for each bulk (indicated by .HIGH and
#' .LOW column name suffix). Total reference allele frequnce "REF_FRQ" is the
#' sum of AD.REF for both bulks divided by total Depth for that SNP. The
#' deltaSNPindex is equal to SNPindex.HIGH - SNPindex.LOW. The GStat column
#' is the calculated G statistic for that SNP.
#' @seealso \code{\link{getG}} for explaination of how G statistic is
#' calculated.
#' \href{http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it}{What
#' is a VCF and how should I interpret it?} for more information on GATK
#' Fields and Genotype Fields
#' @examples df <- ImportFromGATK(filename = file.table,
#' highBulk = highBulkSampleName,
#' lowBulk = lowBulkSampleName,
#' chromList = c("Chr1","Chr4","Chr7"))
#' @export importFromGATK
importFromGATK <- function(file,
highBulk = character(),
lowBulk = character(),
chromList = NULL) {
# first read one line to help define col types
colheader <- read.delim(file, nrows=1, check.names=FALSE)
# identify the sample name specific int and chr columns
int_matches <- grep('DP|GQ', names(colheader), value=TRUE)
chr_matches <- grep('\\.AD', names(colheader), value=TRUE)
# create cols_spec class definitions
int_cols <- do.call(readr::cols, setNames(
rep(list(readr::col_integer()), length(int_matches)),
int_matches))$cols
chr_cols <- do.call(readr::cols, setNames(
rep(list(readr::col_character()), length(chr_matches)),
chr_matches))$cols
col_defs <- readr::cols(CHROM = "c", POS = "i")
col_defs$cols <- c(readr::cols(CHROM = "c", POS = "i")$cols,
int_cols,
chr_cols
)
SNPset <- readr::read_tsv(file = file,
col_names = TRUE,
guess_max = 10000,
col_types = col_defs)
if (!all(
c(
"CHROM",
"POS",
paste0(highBulk, ".AD"),
paste0(lowBulk, ".AD"),
paste0(highBulk, ".DP"),
paste0(lowBulk, ".DP")
) %in% names(SNPset))) {
stop("One of the required fields is missing. Check your table file.")
}
# rename columns based on bulk names and flip headers (ie HIGH.AD -> AD.HIGH to match the rest of the functions
colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")] <-
gsub(pattern = highBulk,
replacement = "HIGH",
x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])
colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")] <-
gsub(pattern = lowBulk,
replacement = "LOW",
x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])
colnames(SNPset) <-
sapply(strsplit(colnames(SNPset), "[.]"),
function(x) {paste0(rev(x),collapse = '.')})
#Keep only wanted chromosomes
if (!is.null(chromList)) {
message("Removing the following chromosomes: ", paste(unique(SNPset$CHROM)[!unique(SNPset$CHROM) %in% chromList], collapse = ", "))
SNPset <- SNPset[SNPset$CHROM %in% chromList, ]
}
#arrange the chromosomes by natural order sort, eg Chr1, Chr10, Chr2 >>> Chr1, Chr2, Chr10
SNPset$CHROM <-
factor(SNPset$CHROM, levels = gtools::mixedsort(unique(SNPset$CHROM)))
SNPset <- SNPset %>%
tidyr::separate(
col = AD.LOW,
into = "AD_REF.LOW",
sep = ",",
extra = "drop",
convert = TRUE
) %>%
tidyr::separate(
col = AD.HIGH,
into = "AD_REF.HIGH",
sep = ",",
extra = "drop",
convert = TRUE
) %>%
dplyr::mutate(
AD_ALT.HIGH = DP.HIGH - AD_REF.HIGH,
AD_ALT.LOW = DP.LOW - AD_REF.LOW,
SNPindex.HIGH = AD_ALT.HIGH / DP.HIGH,
SNPindex.LOW = AD_ALT.LOW / DP.LOW,
REF_FRQ = (AD_REF.HIGH + AD_REF.LOW) / (DP.HIGH + DP.LOW),
deltaSNP = SNPindex.HIGH - SNPindex.LOW
) %>%
dplyr::select(
-dplyr::contains("HIGH"),
-dplyr::contains("LOW"),
-dplyr::one_of("deltaSNP", "REF_FRQ"),
dplyr::matches("AD.*.LOW"),
dplyr::contains("LOW"),
dplyr::matches("AD.*.HIGH"),
dplyr::contains("HIGH"),
dplyr::everything()
)
return(as.data.frame(SNPset))
}
#' Import SNP data from a delimited file
#'
#' After importing the data from a delimited file, the function then calculates
#' total reference allele frequency for both bulks together, the delta SNP index
#' (i.e. SNP index of the low bulk subtracted from the SNP index of the high
#' bulk), the G statistic and returns a data frame. The required columns in the
#' file are CHROM (Chromosome) and POS (Position) as well as the reference and
#' alternate allele depths (number of reads supporting each allele). The allele
#' depths should be in columns named in this format:
#' \code{AD_(<ALT/REF>).<sampleName>}. For example, the column for alternate
#' allele depth for a high bulk sample named "sample1", should be
#' "AD_ALT.sample1". Any other columns describing the SNPs are allowed, ie the
#' actual allele calls, or a quality score. If the column is Bulk specific, It
#' should be named \code{columnName.sampleName}, i.e "QUAL.sample1".
#'
#' @param file The name of the file which the data are to be read from.
#' @param highBulk The sample name of the High Bulk. Defaults to "HIGH"
#' @param lowBulk The sample name of the Low Bulk. Defaults to "LOW"
#' @param chromList a string vector of the chromosomes to be used in the
#' analysis. Useful for filtering out unwanted contigs etc.
#' @param sep the field separator character. Values on each line of the file are
#' separated by this character. Default is for csv file ie ",".
#' @return Returns a data frame containing columns for per bulk total Read depth (DP),
#' Reference Allele Depth (AD_REF) and Alternative Allele Depth (AD_ALT), any
#' other SNP associated columns in the file, and SNPindex for each bulk
#' (indicated by .HIGH and .LOW column name suffix). Total reference allele
#' frequnce "REF_FRQ" is the sum of AD_REF for both bulks divided by total
#' Depth for that SNP. The deltaSNPindex is equal to SNPindex.HIGH -
#' SNPindex.LOW.
#'
#' @export importFromTable
importFromTable <-
function(file,
highBulk = "HIGH",
lowBulk = "LOW",
chromList = NULL,
sep = ",") {
SNPset <-
readr::read_delim(
file = file,
delim = sep,
col_names = TRUE,
col_types = readr::cols(
.default = readr::col_guess(),
CHROM = "c",
POS = "i"
)
)
# check CHROM
if (!"CHROM" %in% names(SNPset)) {
stop("No 'CHROM' coloumn found.")
}
# check POS
if (!"POS" %in% names(SNPset)) {
stop("No 'POS' coloumn found.")
}
# check AD_REF.HIGH
if (!paste0("AD_REF.", highBulk) %in% names(SNPset)) {
stop(
"No High Bulk AD_REF coloumn found. Column should be named 'AD_REF.highBulkName'."
)
}
# check AD_REF.LOW
if (!paste0("AD_REF.", lowBulk) %in% names(SNPset)) {
stop("No Low Bulk AD_REF coloumn found. Column should be named 'AD_REF.lowBulkName'.")
}
#check AD_ALT.HIGH
if (!paste0("AD_ALT.", highBulk) %in% names(SNPset)) {
stop(
"No High Bulk AD_REF coloumn found. Column should be named 'AD_ALT.highBulkName'."
)
}
# check AD_ALT.LOW
if (!paste0("AD_ALT.", lowBulk) %in% names(SNPset)) {
stop("No Low Bulk AD_ALT coloumn found. Column should be named 'AD_ALT.lowBulkName'.")
}
# Keep only wanted chromosomes
if (!is.null(chromList)) {
message("Removing the following chromosomes: ",
paste(unique(SNPset$CHROM)[!unique(SNPset$CHROM) %in% chromList], collapse = ", "))
SNPset <- SNPset[SNPset$CHROM %in% chromList, ]
}
# arrange the chromosomes by natural order sort, eg Chr1, Chr10, Chr2 >>> Chr1, Chr2, Chr10
SNPset$CHROM <-
factor(SNPset$CHROM, levels = gtools::mixedsort(unique(SNPset$CHROM)))
# Rename columns
message("Renaming the following columns: ",
paste(colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")][grep(highBulk, x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])], collapse = ", "))
colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")] <-
gsub(pattern = highBulk,
replacement = "HIGH",
x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])
message("Renaming the following columns: ",
paste(colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")][grep(lowBulk, x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])], collapse = ", "))
colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")] <-
gsub(pattern = lowBulk,
replacement = "LOW",
x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])
# calculate DPs
SNPset <- SNPset %>%
dplyr::mutate(
DP.HIGH = AD_REF.HIGH + AD_ALT.HIGH,
DP.LOW = AD_REF.LOW + AD_ALT.LOW,
SNPindex.HIGH = AD_ALT.HIGH / DP.HIGH,
SNPindex.LOW = AD_ALT.LOW / DP.LOW,
REF_FRQ = (AD_REF.HIGH + AD_REF.LOW) / (DP.HIGH + DP.LOW),
deltaSNP = SNPindex.HIGH - SNPindex.LOW
) %>%
dplyr::select(
-dplyr::contains("HIGH"),-dplyr::contains("LOW"),-dplyr::one_of("deltaSNP", "REF_FRQ"),
dplyr::matches("AD.*.LOW"),
dplyr::contains("LOW"),
dplyr::matches("AD.*.HIGH"),
dplyr::contains("HIGH"),
dplyr::everything()
)
return(as.data.frame(SNPset))
}
## not exported still only works for GATK...
importFromVCF <- function(file,
highBulk = character(),
lowBulk = character(),
chromList = NULL) {
vcf <- vcfR::read.vcfR(file = file)
message("Keeping SNPs that pass all filters")
vcf <- vcf[vcf@fix[, "FILTER"] == "PASS"]
fix <- dplyr::as_tibble(vcf@fix[, c("CHROM", "POS", "REF", "ALT")]) %>% mutate(Key = seq(1:nrow(.)))
# if (!all(
# c(
# "CHROM",
# "POS",
# paste0(highBulk, ".AD"),
# paste0(lowBulk, ".AD"),
# paste0(highBulk, ".DP"),
# paste0(lowBulk, ".DP")
# ) %in% names(SNPset))) {
# stop("One of the required fields is missing. Check your VCF file.")
# }
tidy_gt <- extract_gt_tidy(vcf, format_fields = c("AD", "DP", "GQ"), gt_column_prepend = "", alleles = FALSE)
SNPset <- tidy_gt %>%
filter(Indiv == LowBulk) %>% select(-Indiv) %>%
dplyr::left_join(select(filter(tidy_gt, Indiv == HighBulk),-Indiv),
by = "Key",
suffix = c(".LOW", ".HIGH")) %>%
tidyr::separate(
col = "AD.LOW",
into = c("AD_REF.LOW", "AD_ALT.LOW"),
sep = ",",
extra = "merge",
convert = TRUE
) %>%
tidyr::separate(
col = "AD.HIGH",
into = c("AD_REF.HIGH", "AD_ALT.HIGH"),
sep = ",",
extra = "merge",
convert = TRUE
) %>%
dplyr::full_join(x = fix, by = "Key") %>%
dplyr::mutate(
AD_ALT.HIGH = DP.HIGH - AD_REF.HIGH,
AD_ALT.LOW = DP.LOW - AD_REF.LOW,
SNPindex.HIGH = AD_ALT.HIGH / DP.HIGH,
SNPindex.LOW = AD_ALT.LOW / DP.LOW,
REF_FRQ = (AD_REF.HIGH + AD_REF.LOW) / (DP.HIGH + DP.LOW),
deltaSNP = SNPindex.HIGH - SNPindex.LOW
) %>%
select(-Key)
#Keep only wanted chromosomes
if (!is.null(chromList)) {
message("Removing the following chromosomes: ", paste(unique(SNPset$CHROM)[!unique(SNPset$CHROM) %in% chromList], collapse = ", "))
SNPset <- SNPset[SNPset$CHROM %in% chromList, ]
}
as.data.frame(SNPset)
}
#' Filter SNPs based on read depth and quality
#'
#' Use filtering paramaters to filter out high and low depth reads as well as
#' low Genotype Quality as defined by GATK. All filters are optional but recommended.
#'
#' @param SNPset The data frame imported by \code{ImportFromGATK}
#' @param refAlleleFreq A numeric < 1. This will filter out SNPs with a
#' Reference Allele Frequency less than \code{refAlleleFreq} and greater than
#' 1 - \code{refAlleleFreq}. Eg. \code{refAlleleFreq = 0.3} will keep SNPs
#' with 0.3 <= REF_FRQ <= 0.7
#' @param filterAroundMedianDepth Filters total SNP read depth for both bulks. A
#' median and median absolute deviation (MAD) of depth will be calculated.
#' SNPs with read depth greater or less than \code{filterAroundMedianDepth}
#' MADs away from the median will be filtered.
#' @param minTotalDepth The minimum total read depth for a SNP (counting both
#' bulks)
#' @param maxTotalDepth The maximum total read depth for a SNP (counting both
#' bulks)
#' @param minSampleDepth The minimum read depth for a SNP in each bulk
#' @param depthDifference The maximum absolute difference in read depth between the bulks.
#' @param minGQ The minimum Genotype Quality as set by GATK. This is a measure
#' of how confident GATK was with the assigned genotype (i.e. homozygous ref,
#' heterozygous, homozygous alt). See
#' \href{http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it}{What
#' is a VCF and how should I interpret it?}
#' @param verbose logical. If \code{TRUE} will report number of SNPs filtered in
#' each step.
#' @return Returns a subset of the data frame supplied which meets the filtering
#' conditions applied by the selected parameters. If \code{verbose} is
#' \code{TRUE} the function reports the number of SNPs filtered in each step
#' as well as the initiatl number of SNPs, the total number of SNPs filtered
#' and the remaining number.
#'
#' @seealso See \code{\link[stats]{mad}} for explaination of calculation of
#' median absolute deviation.
#' \href{http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it}{What
#' is a VCF and how should I interpret it?} for more information on GATK
#' Fields and Genotype Fields
#' @examples df_filt <- FilterSNPs(
#' df,
#' refAlleleFreq = 0.3,
#' minTotalDepth = 40,
#' maxTotalDepth = 80,
#' minSampleDepth = 20,
#' minGQ = 99,
#' verbose = TRUE
#' )
#'
#' @export filterSNPs
filterSNPs <- function(SNPset,
refAlleleFreq,
filterAroundMedianDepth,
minTotalDepth,
maxTotalDepth,
minSampleDepth,
depthDifference,
minGQ,
verbose = TRUE) {
org_count <- nrow(SNPset)
count <- nrow(SNPset)
# Filter by total reference allele frequency
if (!missing(refAlleleFreq)) {
if (verbose) {
message(
"Filtering by reference allele frequency: ",
refAlleleFreq,
" <= REF_FRQ <= ",
1 - refAlleleFreq
)
}
SNPset <- dplyr::filter(SNPset, SNPset$REF_FRQ < 1 - refAlleleFreq &
SNPset$REF_FRQ > refAlleleFreq)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
#Total read depth filtering
if (!missing(filterAroundMedianDepth)) {
# filter by Read depth for each SNP FilterByMAD MADs around the median
madDP <-
mad(
x = (SNPset$DP.HIGH + SNPset$DP.LOW),
constant = 1,
na.rm = TRUE
)
medianDP <-
median(x = (SNPset$DP.HIGH + SNPset$DP.LOW),
na.rm = TRUE)
maxDP <- medianDP + filterAroundMedianDepth * madDP
minDP <- medianDP - filterAroundMedianDepth * madDP
SNPset <- dplyr::filter(SNPset, (DP.HIGH + DP.LOW) <= maxDP &
(DP.HIGH + DP.LOW) >= minDP)
if(verbose) {message("Filtering by total read depth: ",
filterAroundMedianDepth,
" MADs arround the median: ", minDP, " <= Total DP <= ", maxDP)
message("...Filtered ", count - nrow(SNPset), " SNPs")}
count <- nrow(SNPset)
}
if (!missing(minTotalDepth)) {
# Filter by minimum total SNP depth
if (verbose) {
message("Filtering by total sample read depth: Total DP >= ",
minTotalDepth)
}
SNPset <-
dplyr::filter(SNPset, (DP.HIGH + DP.LOW) >= minTotalDepth)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
if (!missing(maxTotalDepth)) {
# Filter by maximum total SNP depth
if (verbose) {
message("Filtering by total sample read depth: Total DP <= ",
maxTotalDepth)
}
SNPset <-
dplyr::filter(SNPset, (DP.HIGH + DP.LOW) <= maxTotalDepth)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
# Filter by min read depth in either sample
if (!missing(minSampleDepth)) {
if (verbose) {
message("Filtering by per sample read depth: DP >= ",
minSampleDepth)
}
SNPset <-
dplyr::filter(SNPset, DP.HIGH >= minSampleDepth &
SNPset$DP.LOW >= minSampleDepth)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
# Filter by Genotype Quality
if (!missing(minGQ)) {
if (all(c("GQ.LOW", "GQ.HIGH") %in% names(SNPset))) {
if (verbose) {
message("Filtering by Genotype Quality: GQ >= ", minGQ)
}
SNPset <-
dplyr::filter(SNPset, GQ.LOW >= minGQ & GQ.HIGH >= minGQ)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)}
else {
message("GQ columns not found. Skipping...")
}
}
# Filter by difference between high and low bulks
if (!missing(depthDifference)) {
if (verbose) {
message("Filtering by difference between bulks <= ",
depthDifference)
}
SNPset <-
dplyr::filter(SNPset, abs(DP.HIGH - DP.LOW) <= depthDifference)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
# #Filter SNP Clusters
# if (!is.null(SNPsInCluster) & !is.null(ClusterWin)) {
# tmp <- which(diff(SNPset$POS, SNPsInCluster-1) < ClusterWin)
# message("...Filtered ", count - nrow(SNPset), " SNPs")
# count <- nrow(SNPset)
# }
if (verbose) {
message(
"Original SNP number: ",
org_count,
", Filtered: ",
org_count - count,
", Remaining: ",
count
)
}
return(as.data.frame(SNPset))
}
bmansfeld/QTLseqR documentation built on Jan. 25, 2020, 8:52 p.m.
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Defines functions importFromGATK importFromTable importFromVCF
Documented in importFromGATK importFromTable
#' Imports SNP data from GATK VariablesToTable output
#'
#' Imports SNP data from the output of the
#' \href{https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_VariantsToTable.php}{VariantsToTable}
#' function in GATK. After importing the data, the function then calculates
#' total reference allele frequency for both bulks together, the delta SNP index
#' (i.e. SNP index of the low bulk subtracted from the SNP index of the high
#' bulk), the G statistic and returns a data frame. The required GATK fields
#' (-F) are CHROM (Chromosome) and POS (Position). The required Genotype fields
#' (-GF) are AD (Allele Depth), DP (Depth). Recommended
#' fields are REF (Reference allele) and ALT (Alternative allele) Recommended
#' Genotype feilds are PL (Phred-scaled likelihoods) and GQ (Genotype Quality).
#'
#' @param file The name of the GATK VariablesToTable output .table file which the
#' data are to be read from.
#' @param highBulk The sample name of the High Bulk
#' @param lowBulk The sample name of the Low Bulk
#' @param chromList a string vector of the chromosomes to be used in the
#' analysis. Useful for filtering out unwanted contigs etc.
#' @return Returns a data frame containing columns for Read depth (DP),
#' Reference Allele Depth (AD_REF) and Alternative Allele Depth (AD_ALT),
#' Genoytype Quality (GQ) and SNPindex for each bulk (indicated by .HIGH and
#' .LOW column name suffix). Total reference allele frequnce "REF_FRQ" is the
#' sum of AD.REF for both bulks divided by total Depth for that SNP. The
#' deltaSNPindex is equal to SNPindex.HIGH - SNPindex.LOW. The GStat column
#' is the calculated G statistic for that SNP.
#' @seealso \code{\link{getG}} for explaination of how G statistic is
#' calculated.
#' \href{http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it}{What
#' is a VCF and how should I interpret it?} for more information on GATK
#' Fields and Genotype Fields
#' @examples df <- ImportFromGATK(filename = file.table,
#' highBulk = highBulkSampleName,
#' lowBulk = lowBulkSampleName,
#' chromList = c("Chr1","Chr4","Chr7"))
#' @export importFromGATK
importFromGATK <- function(file,
highBulk = character(),
lowBulk = character(),
chromList = NULL) {
# first read one line to help define col types
colheader <- read.delim(file, nrows=1, check.names=FALSE)
# identify the sample name specific int and chr columns
int_matches <- grep('DP|GQ', names(colheader), value=TRUE)
chr_matches <- grep('\\.AD', names(colheader), value=TRUE)
# create cols_spec class definitions
int_cols <- do.call(readr::cols, setNames(
rep(list(readr::col_integer()), length(int_matches)),
int_matches))$cols
chr_cols <- do.call(readr::cols, setNames(
rep(list(readr::col_character()), length(chr_matches)),
chr_matches))$cols
col_defs <- readr::cols(CHROM = "c", POS = "i")
col_defs$cols <- c(readr::cols(CHROM = "c", POS = "i")$cols,
int_cols,
chr_cols
)
SNPset <- readr::read_tsv(file = file,
col_names = TRUE,
guess_max = 10000,
col_types = col_defs)
if (!all(
c(
"CHROM",
"POS",
paste0(highBulk, ".AD"),
paste0(lowBulk, ".AD"),
paste0(highBulk, ".DP"),
paste0(lowBulk, ".DP")
) %in% names(SNPset))) {
stop("One of the required fields is missing. Check your table file.")
}
# rename columns based on bulk names and flip headers (ie HIGH.AD -> AD.HIGH to match the rest of the functions
colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")] <-
gsub(pattern = highBulk,
replacement = "HIGH",
x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])
colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")] <-
gsub(pattern = lowBulk,
replacement = "LOW",
x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])
colnames(SNPset) <-
sapply(strsplit(colnames(SNPset), "[.]"),
function(x) {paste0(rev(x),collapse = '.')})
#Keep only wanted chromosomes
if (!is.null(chromList)) {
message("Removing the following chromosomes: ", paste(unique(SNPset$CHROM)[!unique(SNPset$CHROM) %in% chromList], collapse = ", "))
SNPset <- SNPset[SNPset$CHROM %in% chromList, ]
}
#arrange the chromosomes by natural order sort, eg Chr1, Chr10, Chr2 >>> Chr1, Chr2, Chr10
SNPset$CHROM <-
factor(SNPset$CHROM, levels = gtools::mixedsort(unique(SNPset$CHROM)))
SNPset <- SNPset %>%
tidyr::separate(
col = AD.LOW,
into = "AD_REF.LOW",
sep = ",",
extra = "drop",
convert = TRUE
) %>%
tidyr::separate(
col = AD.HIGH,
into = "AD_REF.HIGH",
sep = ",",
extra = "drop",
convert = TRUE
) %>%
dplyr::mutate(
AD_ALT.HIGH = DP.HIGH - AD_REF.HIGH,
AD_ALT.LOW = DP.LOW - AD_REF.LOW,
SNPindex.HIGH = AD_ALT.HIGH / DP.HIGH,
SNPindex.LOW = AD_ALT.LOW / DP.LOW,
REF_FRQ = (AD_REF.HIGH + AD_REF.LOW) / (DP.HIGH + DP.LOW),
deltaSNP = SNPindex.HIGH - SNPindex.LOW
) %>%
dplyr::select(
-dplyr::contains("HIGH"),
-dplyr::contains("LOW"),
-dplyr::one_of("deltaSNP", "REF_FRQ"),
dplyr::matches("AD.*.LOW"),
dplyr::contains("LOW"),
dplyr::matches("AD.*.HIGH"),
dplyr::contains("HIGH"),
dplyr::everything()
)
return(as.data.frame(SNPset))
}
#' Import SNP data from a delimited file
#'
#' After importing the data from a delimited file, the function then calculates
#' total reference allele frequency for both bulks together, the delta SNP index
#' (i.e. SNP index of the low bulk subtracted from the SNP index of the high
#' bulk), the G statistic and returns a data frame. The required columns in the
#' file are CHROM (Chromosome) and POS (Position) as well as the reference and
#' alternate allele depths (number of reads supporting each allele). The allele
#' depths should be in columns named in this format:
#' \code{AD_(<ALT/REF>).<sampleName>}. For example, the column for alternate
#' allele depth for a high bulk sample named "sample1", should be
#' "AD_ALT.sample1". Any other columns describing the SNPs are allowed, ie the
#' actual allele calls, or a quality score. If the column is Bulk specific, It
#' should be named \code{columnName.sampleName}, i.e "QUAL.sample1".
#'
#' @param file The name of the file which the data are to be read from.
#' @param highBulk The sample name of the High Bulk. Defaults to "HIGH"
#' @param lowBulk The sample name of the Low Bulk. Defaults to "LOW"
#' @param chromList a string vector of the chromosomes to be used in the
#' analysis. Useful for filtering out unwanted contigs etc.
#' @param sep the field separator character. Values on each line of the file are
#' separated by this character. Default is for csv file ie ",".
#' @return Returns a data frame containing columns for per bulk total Read depth (DP),
#' Reference Allele Depth (AD_REF) and Alternative Allele Depth (AD_ALT), any
#' other SNP associated columns in the file, and SNPindex for each bulk
#' (indicated by .HIGH and .LOW column name suffix). Total reference allele
#' frequnce "REF_FRQ" is the sum of AD_REF for both bulks divided by total
#' Depth for that SNP. The deltaSNPindex is equal to SNPindex.HIGH -
#' SNPindex.LOW.
#'
#' @export importFromTable
importFromTable <-
function(file,
highBulk = "HIGH",
lowBulk = "LOW",
chromList = NULL,
sep = ",") {
SNPset <-
readr::read_delim(
file = file,
delim = sep,
col_names = TRUE,
col_types = readr::cols(
.default = readr::col_guess(),
CHROM = "c",
POS = "i"
)
)
# check CHROM
if (!"CHROM" %in% names(SNPset)) {
stop("No 'CHROM' coloumn found.")
}
# check POS
if (!"POS" %in% names(SNPset)) {
stop("No 'POS' coloumn found.")
}
# check AD_REF.HIGH
if (!paste0("AD_REF.", highBulk) %in% names(SNPset)) {
stop(
"No High Bulk AD_REF coloumn found. Column should be named 'AD_REF.highBulkName'."
)
}
# check AD_REF.LOW
if (!paste0("AD_REF.", lowBulk) %in% names(SNPset)) {
stop("No Low Bulk AD_REF coloumn found. Column should be named 'AD_REF.lowBulkName'.")
}
#check AD_ALT.HIGH
if (!paste0("AD_ALT.", highBulk) %in% names(SNPset)) {
stop(
"No High Bulk AD_REF coloumn found. Column should be named 'AD_ALT.highBulkName'."
)
}
# check AD_ALT.LOW
if (!paste0("AD_ALT.", lowBulk) %in% names(SNPset)) {
stop("No Low Bulk AD_ALT coloumn found. Column should be named 'AD_ALT.lowBulkName'.")
}
# Keep only wanted chromosomes
if (!is.null(chromList)) {
message("Removing the following chromosomes: ",
paste(unique(SNPset$CHROM)[!unique(SNPset$CHROM) %in% chromList], collapse = ", "))
SNPset <- SNPset[SNPset$CHROM %in% chromList, ]
}
# arrange the chromosomes by natural order sort, eg Chr1, Chr10, Chr2 >>> Chr1, Chr2, Chr10
SNPset$CHROM <-
factor(SNPset$CHROM, levels = gtools::mixedsort(unique(SNPset$CHROM)))
# Rename columns
message("Renaming the following columns: ",
paste(colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")][grep(highBulk, x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])], collapse = ", "))
colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")] <-
gsub(pattern = highBulk,
replacement = "HIGH",
x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])
message("Renaming the following columns: ",
paste(colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")][grep(lowBulk, x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])], collapse = ", "))
colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")] <-
gsub(pattern = lowBulk,
replacement = "LOW",
x = colnames(SNPset)[!colnames(SNPset) %in% c("CHROM", "POS", "REF", "ALT")])
# calculate DPs
SNPset <- SNPset %>%
dplyr::mutate(
DP.HIGH = AD_REF.HIGH + AD_ALT.HIGH,
DP.LOW = AD_REF.LOW + AD_ALT.LOW,
SNPindex.HIGH = AD_ALT.HIGH / DP.HIGH,
SNPindex.LOW = AD_ALT.LOW / DP.LOW,
REF_FRQ = (AD_REF.HIGH + AD_REF.LOW) / (DP.HIGH + DP.LOW),
deltaSNP = SNPindex.HIGH - SNPindex.LOW
) %>%
dplyr::select(
-dplyr::contains("HIGH"),-dplyr::contains("LOW"),-dplyr::one_of("deltaSNP", "REF_FRQ"),
dplyr::matches("AD.*.LOW"),
dplyr::contains("LOW"),
dplyr::matches("AD.*.HIGH"),
dplyr::contains("HIGH"),
dplyr::everything()
)
return(as.data.frame(SNPset))
}
## not exported still only works for GATK...
importFromVCF <- function(file,
highBulk = character(),
lowBulk = character(),
chromList = NULL) {
vcf <- vcfR::read.vcfR(file = file)
message("Keeping SNPs that pass all filters")
vcf <- vcf[vcf@fix[, "FILTER"] == "PASS"]
fix <- dplyr::as_tibble(vcf@fix[, c("CHROM", "POS", "REF", "ALT")]) %>% mutate(Key = seq(1:nrow(.)))
# if (!all(
# c(
# "CHROM",
# "POS",
# paste0(highBulk, ".AD"),
# paste0(lowBulk, ".AD"),
# paste0(highBulk, ".DP"),
# paste0(lowBulk, ".DP")
# ) %in% names(SNPset))) {
# stop("One of the required fields is missing. Check your VCF file.")
# }
tidy_gt <- extract_gt_tidy(vcf, format_fields = c("AD", "DP", "GQ"), gt_column_prepend = "", alleles = FALSE)
SNPset <- tidy_gt %>%
filter(Indiv == LowBulk) %>% select(-Indiv) %>%
dplyr::left_join(select(filter(tidy_gt, Indiv == HighBulk),-Indiv),
by = "Key",
suffix = c(".LOW", ".HIGH")) %>%
tidyr::separate(
col = "AD.LOW",
into = c("AD_REF.LOW", "AD_ALT.LOW"),
sep = ",",
extra = "merge",
convert = TRUE
) %>%
tidyr::separate(
col = "AD.HIGH",
into = c("AD_REF.HIGH", "AD_ALT.HIGH"),
sep = ",",
extra = "merge",
convert = TRUE
) %>%
dplyr::full_join(x = fix, by = "Key") %>%
dplyr::mutate(
AD_ALT.HIGH = DP.HIGH - AD_REF.HIGH,
AD_ALT.LOW = DP.LOW - AD_REF.LOW,
SNPindex.HIGH = AD_ALT.HIGH / DP.HIGH,
SNPindex.LOW = AD_ALT.LOW / DP.LOW,
REF_FRQ = (AD_REF.HIGH + AD_REF.LOW) / (DP.HIGH + DP.LOW),
deltaSNP = SNPindex.HIGH - SNPindex.LOW
) %>%
select(-Key)
#Keep only wanted chromosomes
if (!is.null(chromList)) {
message("Removing the following chromosomes: ", paste(unique(SNPset$CHROM)[!unique(SNPset$CHROM) %in% chromList], collapse = ", "))
SNPset <- SNPset[SNPset$CHROM %in% chromList, ]
}
as.data.frame(SNPset)
}
#' Filter SNPs based on read depth and quality
#'
#' Use filtering paramaters to filter out high and low depth reads as well as
#' low Genotype Quality as defined by GATK. All filters are optional but recommended.
#'
#' @param SNPset The data frame imported by \code{ImportFromGATK}
#' @param refAlleleFreq A numeric < 1. This will filter out SNPs with a
#' Reference Allele Frequency less than \code{refAlleleFreq} and greater than
#' 1 - \code{refAlleleFreq}. Eg. \code{refAlleleFreq = 0.3} will keep SNPs
#' with 0.3 <= REF_FRQ <= 0.7
#' @param filterAroundMedianDepth Filters total SNP read depth for both bulks. A
#' median and median absolute deviation (MAD) of depth will be calculated.
#' SNPs with read depth greater or less than \code{filterAroundMedianDepth}
#' MADs away from the median will be filtered.
#' @param minTotalDepth The minimum total read depth for a SNP (counting both
#' bulks)
#' @param maxTotalDepth The maximum total read depth for a SNP (counting both
#' bulks)
#' @param minSampleDepth The minimum read depth for a SNP in each bulk
#' @param depthDifference The maximum absolute difference in read depth between the bulks.
#' @param minGQ The minimum Genotype Quality as set by GATK. This is a measure
#' of how confident GATK was with the assigned genotype (i.e. homozygous ref,
#' heterozygous, homozygous alt). See
#' \href{http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it}{What
#' is a VCF and how should I interpret it?}
#' @param verbose logical. If \code{TRUE} will report number of SNPs filtered in
#' each step.
#' @return Returns a subset of the data frame supplied which meets the filtering
#' conditions applied by the selected parameters. If \code{verbose} is
#' \code{TRUE} the function reports the number of SNPs filtered in each step
#' as well as the initiatl number of SNPs, the total number of SNPs filtered
#' and the remaining number.
#'
#' @seealso See \code{\link[stats]{mad}} for explaination of calculation of
#' median absolute deviation.
#' \href{http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it}{What
#' is a VCF and how should I interpret it?} for more information on GATK
#' Fields and Genotype Fields
#' @examples df_filt <- FilterSNPs(
#' df,
#' refAlleleFreq = 0.3,
#' minTotalDepth = 40,
#' maxTotalDepth = 80,
#' minSampleDepth = 20,
#' minGQ = 99,
#' verbose = TRUE
#' )
#'
#' @export filterSNPs
filterSNPs <- function(SNPset,
refAlleleFreq,
filterAroundMedianDepth,
minTotalDepth,
maxTotalDepth,
minSampleDepth,
depthDifference,
minGQ,
verbose = TRUE) {
org_count <- nrow(SNPset)
count <- nrow(SNPset)
# Filter by total reference allele frequency
if (!missing(refAlleleFreq)) {
if (verbose) {
message(
"Filtering by reference allele frequency: ",
refAlleleFreq,
" <= REF_FRQ <= ",
1 - refAlleleFreq
)
}
SNPset <- dplyr::filter(SNPset, SNPset$REF_FRQ < 1 - refAlleleFreq &
SNPset$REF_FRQ > refAlleleFreq)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
#Total read depth filtering
if (!missing(filterAroundMedianDepth)) {
# filter by Read depth for each SNP FilterByMAD MADs around the median
madDP <-
mad(
x = (SNPset$DP.HIGH + SNPset$DP.LOW),
constant = 1,
na.rm = TRUE
)
medianDP <-
median(x = (SNPset$DP.HIGH + SNPset$DP.LOW),
na.rm = TRUE)
maxDP <- medianDP + filterAroundMedianDepth * madDP
minDP <- medianDP - filterAroundMedianDepth * madDP
SNPset <- dplyr::filter(SNPset, (DP.HIGH + DP.LOW) <= maxDP &
(DP.HIGH + DP.LOW) >= minDP)
if(verbose) {message("Filtering by total read depth: ",
filterAroundMedianDepth,
" MADs arround the median: ", minDP, " <= Total DP <= ", maxDP)
message("...Filtered ", count - nrow(SNPset), " SNPs")}
count <- nrow(SNPset)
}
if (!missing(minTotalDepth)) {
# Filter by minimum total SNP depth
if (verbose) {
message("Filtering by total sample read depth: Total DP >= ",
minTotalDepth)
}
SNPset <-
dplyr::filter(SNPset, (DP.HIGH + DP.LOW) >= minTotalDepth)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
if (!missing(maxTotalDepth)) {
# Filter by maximum total SNP depth
if (verbose) {
message("Filtering by total sample read depth: Total DP <= ",
maxTotalDepth)
}
SNPset <-
dplyr::filter(SNPset, (DP.HIGH + DP.LOW) <= maxTotalDepth)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
# Filter by min read depth in either sample
if (!missing(minSampleDepth)) {
if (verbose) {
message("Filtering by per sample read depth: DP >= ",
minSampleDepth)
}
SNPset <-
dplyr::filter(SNPset, DP.HIGH >= minSampleDepth &
SNPset$DP.LOW >= minSampleDepth)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
# Filter by Genotype Quality
if (!missing(minGQ)) {
if (all(c("GQ.LOW", "GQ.HIGH") %in% names(SNPset))) {
if (verbose) {
message("Filtering by Genotype Quality: GQ >= ", minGQ)
}
SNPset <-
dplyr::filter(SNPset, GQ.LOW >= minGQ & GQ.HIGH >= minGQ)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)}
else {
message("GQ columns not found. Skipping...")
}
}
# Filter by difference between high and low bulks
if (!missing(depthDifference)) {
if (verbose) {
message("Filtering by difference between bulks <= ",
depthDifference)
}
SNPset <-
dplyr::filter(SNPset, abs(DP.HIGH - DP.LOW) <= depthDifference)
if (verbose) {
message("...Filtered ", count - nrow(SNPset), " SNPs")
}
count <- nrow(SNPset)
}
# #Filter SNP Clusters
# if (!is.null(SNPsInCluster) & !is.null(ClusterWin)) {
# tmp <- which(diff(SNPset$POS, SNPsInCluster-1) < ClusterWin)
# message("...Filtered ", count - nrow(SNPset), " SNPs")
# count <- nrow(SNPset)
# }
if (verbose) {
message(
"Original SNP number: ",
org_count,
", Filtered: ",
org_count - count,
", Remaining: ",
count
)
}
return(as.data.frame(SNPset))
}
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