R/mapGapFromOverlap.R

In contiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

# Copyright (c) 2015, Mark Hills
# All rights reserved.

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####################################################################################################
#' mapGapFromOverlap -- function to co-localize strand state changes with assembly gaps 
#' 
#' @param sceFile GRanges object of strand state change locations in BED format 
#' @param gapFile GRanges object of assembly gaps in BED format (can be downloaded from UCSC table browser)
#' @param chrTable GRanges object of chromosome table (product of makeChrTable)
#' @param verbose prints messages to the terminal (default is TRUE)
#' @param overlapNum  Minimal number of strand state changes that overlap with a gap before assembly is cut at that location
#' 
#' @return a GRanges object of all contigs split by regions where the sceFile and gapFile GRanges objects overlap.
#' @import GenomicRanges
#' @import DNAcopy
#' @importFrom BiocGenerics "%in%"
#' @importFrom S4Vectors DataFrame
#' @export
#' @include AllClasses.R
####################################################################################################


mapGapFromOverlap <- function(sceFile,  gapFile, chrTable, verbose=TRUE, overlapNum=4)
{

	#remove names element from chrTable if present
	chrTable$name <- NULL

	hits <- countOverlaps(gapFile, sceFile)

	#append hits to gapFile to show number of SCE events that are coincident with gaps
	gapFile$overlapSCE <- hits

	#if not already, order by chromosome then start location of gap.
	gapFile <- sort(gapFile)

	# For every chromosome that has a gap and a corresponding SCE...
	for(chr in unique(seqnames(sceFile)[seqnames(sceFile) %in% seqnames(gapFile)])  )
	{
		gapPerChr <- gapFile[seqnames(gapFile) == as.character(chr)]
		if(max(gapPerChr$overlapSCE) >= overlapNum)
		{
			CNA.object <- CNA(gapPerChr$overlapSCE, 
							  as.character(seqnames(gapPerChr)), start(gapPerChr))
			smoothed.CNA.object <- smooth.CNA(CNA.object, smooth.region=2)
			segmented <- segment(smoothed.CNA.object, verbose=0)
			segs <- segmented$output
			if(nrow(segs) > 1)
			{
				segs <- segs[which(diff(sign(diff(segs$seg.mean)))==-2)+1,c(2:4, 6)]
				segs <- segs[which(segs$seg.mean >= overlapNum),]
				segs <- GRanges(segs$chrom, IRanges(start=segs$loc.start, end=segs$loc.end))
			}else{
				segs <- gapPerChr[gapPerChr$overlapSCE == max(gapPerChr$overlapSCE)]
			}

			segs$overlapSCE <- NULL
			chrTable <- append(GRanges(chrTable), segs)
		}
	}

	#Now split the assembly where overlaps occur
	chrTable <- disjoin(chrTable)

	chrTable$name <- paste(seqnames(chrTable), ":", start(chrTable), "-", end(chrTable), sep="")
	chrTable <- ChrTable(chrTable)
	return(chrTable)
}