R/mapATR.R
In adamstruck/RECD: Repeat Exansion & Contraction Detection
##' Sorts read pairs into three categories: flanking, facing, and fully repetitive.
##'
##' Description of output files:
##' flanking: read pair completely flank the repeat or are anchored outside the repeat (minimum = margin)
##' facing: one read flanks or is anchored outside the repeat (minimum = margin) while its pair aligned inside the repeat (or didn't meet minimum anchor requirements)
##' fully_repetitive: both reads in pair aligned inside the repeat (or didn't meet minimum anchor requirements)
##' @title mapATR [mapAlignmentsToRepeats]
##' @param con database connection
##' @param table_name name of table in database
##' @param input_file inner_mate_range.tsv file (make sure chr names are compatible with your database)
##' @param imd_dist .insert_length_dist file (i.e. the inner mate distance distribution file for the sample)
##' @param upper_limit values between 0 and 1 will be used to set prob in quantile() and then used to calculate the maximum allowed distance from the repeat. Values greater than 1 will be applied as the maximum. Read pairs whose ends are farther from the repeat than the value set by this parameter will be not be used. [default= 0.95]
##' @param margin minimum bp a read must be anchored outside the repeat [default= read_length/4]
##' @param read_length read length
##' @param min_repeat_length minimum repeat length in reference genome [default= 12]
##' @param output_dir output directory to write results [default= "."]
##' @param append_chr appends "chr" to chromosome names of inner_mate_ranges file if TRUE [default= TRUE]
##' @param overwrite should output files be overwritten? [default= TRUE]
##' @param margin maximum bp overlap between each read and a given repeat repeat [default= read_length/2]
##' @return _flanking, _facing, and _fully_repetitive .tsv files
##' @author Adam Struck
##' @export
mapATR <- function(con, table_name, input_file, imd_dist=NULL, upper_limit=0.95, margin=(read_length/4), read_length, min_repeat_length=12, output_dir=".", append_chr=FALSE, overwrite=TRUE) {
if( file.exists(output_dir) ) {
setwd(output_dir)
} else {
dir.create(output_dir)
setwd(output_dir)
}
chrs <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrM", "chrX", "chrY")
message("Reading in ", input_file, " at ", Sys.time())
passed <- 0
for(i.chr in 1:length(chrs)) {
chr <- chrs[i.chr]
message("Working on chr: ", i.chr , "/", length(chrs), " ", Sys.time())
if(append_chr == TRUE) {
sample <- try(read.table(pipe(sprintf("sed 's/^/chr/g' %s | awk '/%s[\t]/ {print $0}'", input_file, chr))))
if (class(sample) == "try-error") { next }
} else {
sample <- try(read.table(pipe(sprintf("awk '/%s[\t]/ {print $0}' %s", chr, input_file))))
if (class(sample) == "try-error") { next }
}
colnames(sample) <- c("chr", "plus", "minus", "strand", "n")
passed <- passed + 1
flanking.file.header <- c("repeat.id", "inner.mate.distance", "n")
facing.file.header <- c("repeat.id", "side", "distance", "n")
fullrepeat.file.header <- c("repeat.id", "n")
if(passed == 1) {
overwrite.val <- overwrite
fh.flanking <- openOutputFileHandle(input_file, suffix="flanking", header=flanking.file.header, overwrite=overwrite.val)
fh.facing <- openOutputFileHandle(input_file, suffix="facing", header=facing.file.header, overwrite=overwrite.val)
fh.fullrepeat <- openOutputFileHandle(input_file, suffix="fullrepeat", header=fullrepeat.file.header, overwrite=overwrite.val)
} else {
overwrite.val <- FALSE
fh.flanking <- openOutputFileHandle(input_file, suffix="flanking", header=flanking.file.header, overwrite=overwrite.val)
fh.facing <- openOutputFileHandle(input_file, suffix="facing", header=facing.file.header, overwrite=overwrite.val)
fh.fullrepeat <- openOutputFileHandle(input_file, suffix="fullrepeat", header=fullrepeat.file.header, overwrite=overwrite.val)
}
if(upper_limit <= 1) {
if( !is.null(imd_dist) ) {
imd.dist <- read.table(imd_dist, header=TRUE, sep="\t")
names(imd.dist) <- c("inner.mate.distance", "n")
dist <- rep(imd.dist$inner.mate.distance, imd.dist$n)
limits <- quantile(dist, probs=upper_limit)
upper.limit <- limits[[1]]
} else {
stop("You need to supply an inner mate distance distribution file for your sample")
}
} else {
upper.limit <- upper_limit
}
sample.pairs.overlap <- sample[sample$minus < sample$plus,]
sample.pairs.overlap.gr <- GRanges(seqnames=Rle(sample.pairs.overlap$chr), ranges=IRanges(sample.pairs.overlap$minus, sample.pairs.overlap$plus), mcols=sample.pairs.overlap$n)
sample <- sample[sample$minus >= sample$plus,]
sample.gr <- GRanges(seqnames=Rle(sample$chr), ranges=IRanges(sample$plus, sample$minus), mcols=sample$n)
repeats <- dbGetQuery(con, sprintf("select * from %s where chr='%s'", table_name, chr))
repeats <- repeats[(repeats$end-repeats$start) > min_repeat_length,]
repeats.gr <- GRanges(seqnames=Rle(repeats$chr), ranges=IRanges(repeats$start, repeats$end))
message("Read in repeats on ", chr, " from table ", table_name, " at ", Sys.time())
message(paste(capture.output(gc()), collapse="\n"))
overlaps <- BiocGenerics::as.data.frame(findOverlaps(sample.gr, repeats.gr, type="any", maxgap=0L, minoverlap=1L, ignore.strand=TRUE))
uniq.repeats <- unique(overlaps[,2])
if(length(uniq.repeats) > 0) {
message("Found read pairs that overlap repeats on ", chr, " ", Sys.time())
for(i.rep in 1:length(uniq.repeats)) {
rep <- uniq.repeats[i.rep]
if ((i.rep %% 50 == 0) == TRUE) {
message("Working on repeat: ", i.rep , "/", length(uniq.repeats), " ", Sys.time())
}
overlap.subset <- overlaps[overlaps$subjectHits == rep,]
sample.subset <- BiocGenerics::as.data.frame(sample.gr)[overlap.subset$queryHits,]
repeat.subset <- BiocGenerics::as.data.frame(repeats.gr)[rep,]
repeat_id <- paste(repeat.subset$seqname, paste(repeat.subset$start, repeat.subset$end, sep="-"), sep=":")
flanking.results <- getFlanking(sample.subset, repeat.subset, repeat_id, margin, upper.limit)
if(class(flanking.results) == "data.frame") {
writeResults(flanking.results, fh.flanking)
}
facing.results <- getFacing(sample.subset, repeat.subset, repeat_id, margin, upper.limit)
if(class(facing.results) == "data.frame") {
writeResults(facing.results, fh.facing)
}
fullrepeat.results <- getFullRepeats(sample.subset, repeat.subset, repeat_id, margin)
if(class(fullrepeat.results) == "data.frame") {
writeResults(fullrepeat.results, fh.fullrepeat)
}
}
}
### For the cases where minus < plus
message("Working on overlaping reads... ", Sys.time())
overlaps.po <- BiocGenerics::as.data.frame(findOverlaps(sample.pairs.overlap.gr, repeats.gr, type="any", maxgap=0L, minoverlap=1L, ignore.strand=TRUE))
uniq.repeats <- unique(overlaps.po[,2])
if(length(uniq.repeats) > 0) {
for(i.rep in 1:length(uniq.repeats)) {
if ((i.rep %% 50 == 0) == TRUE) {
message("Working on repeat: ", i.rep , "/", length(uniq.repeats), " ", Sys.time())
}
rep <- uniq.repeats[i.rep]
overlap.subset <- overlaps.po[overlaps.po$subjectHits == rep,]
sample.subset <- BiocGenerics::as.data.frame(sample.pairs.overlap.gr)[overlap.subset$queryHits,]
names(sample.subset) <- c("seqnames", "end", "start", "width", "strand", "mcols")
sample.subset$width <- -sample.subset$width
repeat.subset <- BiocGenerics::as.data.frame(repeats.gr)[rep,]
repeat_id <- paste(repeat.subset$seqname, paste(repeat.subset$start, repeat.subset$end, sep="-"), sep=":")
flanking.results <- getFlanking(sample.subset, repeat.subset, repeat_id, margin, upper.limit)
if(class(flanking.results) == "data.frame") {
writeResults(flanking.results, fh.flanking)
}
facing.results <- getFacing(sample.subset, repeat.subset, repeat_id, margin, upper.limit)
if(class(facing.results) == "data.frame") {
writeResults(facing.results, fh.facing)
}
fullrepeat.results <- getFullRepeats(sample.subset, repeat.subset, repeat_id, margin)
if(class(fullrepeat.results) == "data.frame") {
writeResults(fullrepeat.results, fh.fullrepeat)
}
}
}
close(fh.flanking)
close(fh.facing)
close(fh.fullrepeat)
}
}
getFlanking <- function(sample.subset, repeat.subset, repeat_id, margin, upper.limit) {
plus.read.anchored <- sample.subset$start <= (repeat.subset$start + margin)
minus.read.anchored <- sample.subset$end >= (repeat.subset$end - margin)
plus.prox <- ((repeat.subset$start + margin) - sample.subset$start) <= upper.limit
minus.prox <- (sample.subset$end - (repeat.subset$end - margin)) <= upper.limit
plus.conditions <- plus.read.anchored & plus.prox
minus.conditions <- minus.read.anchored & minus.prox
flanking <- sample.subset[(plus.conditions & minus.conditions),]
if(dim(flanking)[1] > 0) {
imds <- rep(flanking$width, flanking$mcols)
n <- table(imds)
inner.mate.distance <- as.integer(names(n))
flanking.results <- data.frame(repeat_id, inner.mate.distance, n=as.vector(n), row.names=NULL)
} else { flanking.results <- NULL }
return(flanking.results)
}
getFacing <- function(sample.subset, repeat.subset, repeat_id, margin, upper.limit) {
plus.read.in.repeat <- sample.subset$start > (repeat.subset$start + margin)
minus.read.outside <- sample.subset$end >= (repeat.subset$end - margin)
minus.prox <- (sample.subset$end - (repeat.subset$end - margin)) <= upper.limit
facing.from.right <- plus.read.in.repeat & minus.read.outside & minus.prox
plus.read.outside <- sample.subset$start <= (repeat.subset$start + margin)
minus.read.in.repeat <- sample.subset$end < (repeat.subset$end - margin)
plus.prox <- ((repeat.subset$start + margin) - sample.subset$start) <= upper.limit
facing.from.left <- plus.read.outside & minus.read.in.repeat & plus.prox
facing <- sample.subset[(facing.from.left | facing.from.right),]
if(dim(facing)[1] > 0) {
from.left.facing <- facing[facing$end < (repeat.subset$end - margin),]
if(dim(from.left.facing)[1] > 0) {
from.left.facing.dist <- from.left.facing$start - repeat.subset$start
from.left.facing.dist <- rep(from.left.facing.dist, from.left.facing$mcols)
left.n <- table(from.left.facing.dist)
from.left.dist.to.rep <- as.integer(names(left.n))
from.left.results <- data.frame(repeat_id, side="left", distance_to_repeat=from.left.dist.to.rep, n=as.vector(left.n), row.names=NULL)
} else { from.left.results <- NULL }
from.right.facing <- facing[facing$start > (repeat.subset$start + margin),]
if(dim(from.right.facing)[1] > 0) {
from.right.facing.dist <- from.right.facing$end - repeat.subset$end
from.right.facing.dist <- rep(from.right.facing.dist, from.right.facing$mcols)
right.n <- table(from.right.facing.dist)
from.right.dist.to.rep <- as.integer(names(right.n))
from.right.results <- data.frame(repeat_id, side="right", distance_to_repeat=from.right.dist.to.rep, n=as.vector(right.n), row.names=NULL)
} else { from.right.results <- NULL}
facing.results <- rbind(from.left.results, from.right.results)
} else { facing.results <- NULL }
return(facing.results)
}
getFullRepeats <- function(sample.subset, repeat.subset, repeat_id, margin) {
plus.read.in.repeat <- sample.subset$start > (repeat.subset$start + margin)
minus.read.in.repeat <- sample.subset$end < (repeat.subset$end - margin)
full_repeat <- sample.subset[(plus.read.in.repeat & minus.read.in.repeat),]
if(dim(full_repeat)[1] > 0) {
n <- sum(sample.subset$mcols)
fullrepeats <- data.frame(repeat_id, n, row.names=NULL)
} else { fullrepeats <- NULL }
return(fullrepeats)
}
adamstruck/RECD documentation built on May 10, 2019, 5:51 a.m.
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##' Sorts read pairs into three categories: flanking, facing, and fully repetitive.
##'
##' Description of output files:
##' flanking: read pair completely flank the repeat or are anchored outside the repeat (minimum = margin)
##' facing: one read flanks or is anchored outside the repeat (minimum = margin) while its pair aligned inside the repeat (or didn't meet minimum anchor requirements)
##' fully_repetitive: both reads in pair aligned inside the repeat (or didn't meet minimum anchor requirements)
##' @title mapATR [mapAlignmentsToRepeats]
##' @param con database connection
##' @param table_name name of table in database
##' @param input_file inner_mate_range.tsv file (make sure chr names are compatible with your database)
##' @param imd_dist .insert_length_dist file (i.e. the inner mate distance distribution file for the sample)
##' @param upper_limit values between 0 and 1 will be used to set prob in quantile() and then used to calculate the maximum allowed distance from the repeat. Values greater than 1 will be applied as the maximum. Read pairs whose ends are farther from the repeat than the value set by this parameter will be not be used. [default= 0.95]
##' @param margin minimum bp a read must be anchored outside the repeat [default= read_length/4]
##' @param read_length read length
##' @param min_repeat_length minimum repeat length in reference genome [default= 12]
##' @param output_dir output directory to write results [default= "."]
##' @param append_chr appends "chr" to chromosome names of inner_mate_ranges file if TRUE [default= TRUE]
##' @param overwrite should output files be overwritten? [default= TRUE]
##' @param margin maximum bp overlap between each read and a given repeat repeat [default= read_length/2]
##' @return _flanking, _facing, and _fully_repetitive .tsv files
##' @author Adam Struck
##' @export
mapATR <- function(con, table_name, input_file, imd_dist=NULL, upper_limit=0.95, margin=(read_length/4), read_length, min_repeat_length=12, output_dir=".", append_chr=FALSE, overwrite=TRUE) {
if( file.exists(output_dir) ) {
setwd(output_dir)
} else {
dir.create(output_dir)
setwd(output_dir)
}
chrs <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrM", "chrX", "chrY")
message("Reading in ", input_file, " at ", Sys.time())
passed <- 0
for(i.chr in 1:length(chrs)) {
chr <- chrs[i.chr]
message("Working on chr: ", i.chr , "/", length(chrs), " ", Sys.time())
if(append_chr == TRUE) {
sample <- try(read.table(pipe(sprintf("sed 's/^/chr/g' %s | awk '/%s[\t]/ {print $0}'", input_file, chr))))
if (class(sample) == "try-error") { next }
} else {
sample <- try(read.table(pipe(sprintf("awk '/%s[\t]/ {print $0}' %s", chr, input_file))))
if (class(sample) == "try-error") { next }
}
colnames(sample) <- c("chr", "plus", "minus", "strand", "n")
passed <- passed + 1
flanking.file.header <- c("repeat.id", "inner.mate.distance", "n")
facing.file.header <- c("repeat.id", "side", "distance", "n")
fullrepeat.file.header <- c("repeat.id", "n")
if(passed == 1) {
overwrite.val <- overwrite
fh.flanking <- openOutputFileHandle(input_file, suffix="flanking", header=flanking.file.header, overwrite=overwrite.val)
fh.facing <- openOutputFileHandle(input_file, suffix="facing", header=facing.file.header, overwrite=overwrite.val)
fh.fullrepeat <- openOutputFileHandle(input_file, suffix="fullrepeat", header=fullrepeat.file.header, overwrite=overwrite.val)
} else {
overwrite.val <- FALSE
fh.flanking <- openOutputFileHandle(input_file, suffix="flanking", header=flanking.file.header, overwrite=overwrite.val)
fh.facing <- openOutputFileHandle(input_file, suffix="facing", header=facing.file.header, overwrite=overwrite.val)
fh.fullrepeat <- openOutputFileHandle(input_file, suffix="fullrepeat", header=fullrepeat.file.header, overwrite=overwrite.val)
}
if(upper_limit <= 1) {
if( !is.null(imd_dist) ) {
imd.dist <- read.table(imd_dist, header=TRUE, sep="\t")
names(imd.dist) <- c("inner.mate.distance", "n")
dist <- rep(imd.dist$inner.mate.distance, imd.dist$n)
limits <- quantile(dist, probs=upper_limit)
upper.limit <- limits[[1]]
} else {
stop("You need to supply an inner mate distance distribution file for your sample")
}
} else {
upper.limit <- upper_limit
}
sample.pairs.overlap <- sample[sample$minus < sample$plus,]
sample.pairs.overlap.gr <- GRanges(seqnames=Rle(sample.pairs.overlap$chr), ranges=IRanges(sample.pairs.overlap$minus, sample.pairs.overlap$plus), mcols=sample.pairs.overlap$n)
sample <- sample[sample$minus >= sample$plus,]
sample.gr <- GRanges(seqnames=Rle(sample$chr), ranges=IRanges(sample$plus, sample$minus), mcols=sample$n)
repeats <- dbGetQuery(con, sprintf("select * from %s where chr='%s'", table_name, chr))
repeats <- repeats[(repeats$end-repeats$start) > min_repeat_length,]
repeats.gr <- GRanges(seqnames=Rle(repeats$chr), ranges=IRanges(repeats$start, repeats$end))
message("Read in repeats on ", chr, " from table ", table_name, " at ", Sys.time())
message(paste(capture.output(gc()), collapse="\n"))
overlaps <- BiocGenerics::as.data.frame(findOverlaps(sample.gr, repeats.gr, type="any", maxgap=0L, minoverlap=1L, ignore.strand=TRUE))
uniq.repeats <- unique(overlaps[,2])
if(length(uniq.repeats) > 0) {
message("Found read pairs that overlap repeats on ", chr, " ", Sys.time())
for(i.rep in 1:length(uniq.repeats)) {
rep <- uniq.repeats[i.rep]
if ((i.rep %% 50 == 0) == TRUE) {
message("Working on repeat: ", i.rep , "/", length(uniq.repeats), " ", Sys.time())
}
overlap.subset <- overlaps[overlaps$subjectHits == rep,]
sample.subset <- BiocGenerics::as.data.frame(sample.gr)[overlap.subset$queryHits,]
repeat.subset <- BiocGenerics::as.data.frame(repeats.gr)[rep,]
repeat_id <- paste(repeat.subset$seqname, paste(repeat.subset$start, repeat.subset$end, sep="-"), sep=":")
flanking.results <- getFlanking(sample.subset, repeat.subset, repeat_id, margin, upper.limit)
if(class(flanking.results) == "data.frame") {
writeResults(flanking.results, fh.flanking)
}
facing.results <- getFacing(sample.subset, repeat.subset, repeat_id, margin, upper.limit)
if(class(facing.results) == "data.frame") {
writeResults(facing.results, fh.facing)
}
fullrepeat.results <- getFullRepeats(sample.subset, repeat.subset, repeat_id, margin)
if(class(fullrepeat.results) == "data.frame") {
writeResults(fullrepeat.results, fh.fullrepeat)
}
}
}
### For the cases where minus < plus
message("Working on overlaping reads... ", Sys.time())
overlaps.po <- BiocGenerics::as.data.frame(findOverlaps(sample.pairs.overlap.gr, repeats.gr, type="any", maxgap=0L, minoverlap=1L, ignore.strand=TRUE))
uniq.repeats <- unique(overlaps.po[,2])
if(length(uniq.repeats) > 0) {
for(i.rep in 1:length(uniq.repeats)) {
if ((i.rep %% 50 == 0) == TRUE) {
message("Working on repeat: ", i.rep , "/", length(uniq.repeats), " ", Sys.time())
}
rep <- uniq.repeats[i.rep]
overlap.subset <- overlaps.po[overlaps.po$subjectHits == rep,]
sample.subset <- BiocGenerics::as.data.frame(sample.pairs.overlap.gr)[overlap.subset$queryHits,]
names(sample.subset) <- c("seqnames", "end", "start", "width", "strand", "mcols")
sample.subset$width <- -sample.subset$width
repeat.subset <- BiocGenerics::as.data.frame(repeats.gr)[rep,]
repeat_id <- paste(repeat.subset$seqname, paste(repeat.subset$start, repeat.subset$end, sep="-"), sep=":")
flanking.results <- getFlanking(sample.subset, repeat.subset, repeat_id, margin, upper.limit)
if(class(flanking.results) == "data.frame") {
writeResults(flanking.results, fh.flanking)
}
facing.results <- getFacing(sample.subset, repeat.subset, repeat_id, margin, upper.limit)
if(class(facing.results) == "data.frame") {
writeResults(facing.results, fh.facing)
}
fullrepeat.results <- getFullRepeats(sample.subset, repeat.subset, repeat_id, margin)
if(class(fullrepeat.results) == "data.frame") {
writeResults(fullrepeat.results, fh.fullrepeat)
}
}
}
close(fh.flanking)
close(fh.facing)
close(fh.fullrepeat)
}
}
getFlanking <- function(sample.subset, repeat.subset, repeat_id, margin, upper.limit) {
plus.read.anchored <- sample.subset$start <= (repeat.subset$start + margin)
minus.read.anchored <- sample.subset$end >= (repeat.subset$end - margin)
plus.prox <- ((repeat.subset$start + margin) - sample.subset$start) <= upper.limit
minus.prox <- (sample.subset$end - (repeat.subset$end - margin)) <= upper.limit
plus.conditions <- plus.read.anchored & plus.prox
minus.conditions <- minus.read.anchored & minus.prox
flanking <- sample.subset[(plus.conditions & minus.conditions),]
if(dim(flanking)[1] > 0) {
imds <- rep(flanking$width, flanking$mcols)
n <- table(imds)
inner.mate.distance <- as.integer(names(n))
flanking.results <- data.frame(repeat_id, inner.mate.distance, n=as.vector(n), row.names=NULL)
} else { flanking.results <- NULL }
return(flanking.results)
}
getFacing <- function(sample.subset, repeat.subset, repeat_id, margin, upper.limit) {
plus.read.in.repeat <- sample.subset$start > (repeat.subset$start + margin)
minus.read.outside <- sample.subset$end >= (repeat.subset$end - margin)
minus.prox <- (sample.subset$end - (repeat.subset$end - margin)) <= upper.limit
facing.from.right <- plus.read.in.repeat & minus.read.outside & minus.prox
plus.read.outside <- sample.subset$start <= (repeat.subset$start + margin)
minus.read.in.repeat <- sample.subset$end < (repeat.subset$end - margin)
plus.prox <- ((repeat.subset$start + margin) - sample.subset$start) <= upper.limit
facing.from.left <- plus.read.outside & minus.read.in.repeat & plus.prox
facing <- sample.subset[(facing.from.left | facing.from.right),]
if(dim(facing)[1] > 0) {
from.left.facing <- facing[facing$end < (repeat.subset$end - margin),]
if(dim(from.left.facing)[1] > 0) {
from.left.facing.dist <- from.left.facing$start - repeat.subset$start
from.left.facing.dist <- rep(from.left.facing.dist, from.left.facing$mcols)
left.n <- table(from.left.facing.dist)
from.left.dist.to.rep <- as.integer(names(left.n))
from.left.results <- data.frame(repeat_id, side="left", distance_to_repeat=from.left.dist.to.rep, n=as.vector(left.n), row.names=NULL)
} else { from.left.results <- NULL }
from.right.facing <- facing[facing$start > (repeat.subset$start + margin),]
if(dim(from.right.facing)[1] > 0) {
from.right.facing.dist <- from.right.facing$end - repeat.subset$end
from.right.facing.dist <- rep(from.right.facing.dist, from.right.facing$mcols)
right.n <- table(from.right.facing.dist)
from.right.dist.to.rep <- as.integer(names(right.n))
from.right.results <- data.frame(repeat_id, side="right", distance_to_repeat=from.right.dist.to.rep, n=as.vector(right.n), row.names=NULL)
} else { from.right.results <- NULL}
facing.results <- rbind(from.left.results, from.right.results)
} else { facing.results <- NULL }
return(facing.results)
}
getFullRepeats <- function(sample.subset, repeat.subset, repeat_id, margin) {
plus.read.in.repeat <- sample.subset$start > (repeat.subset$start + margin)
minus.read.in.repeat <- sample.subset$end < (repeat.subset$end - margin)
full_repeat <- sample.subset[(plus.read.in.repeat & minus.read.in.repeat),]
if(dim(full_repeat)[1] > 0) {
n <- sum(sample.subset$mcols)
fullrepeats <- data.frame(repeat_id, n, row.names=NULL)
} else { fullrepeats <- NULL }
return(fullrepeats)
}
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