mapGapFromOverlap {contiBAIT} | R Documentation |
mapGapFromOverlap – function to co-localize strand state changes with assembly gaps
mapGapFromOverlap(sceFile, gapFile, chrTable, verbose = TRUE, overlapNum = 4)
sceFile |
GRanges object of strand state change locations in BED format |
gapFile |
GRanges object of assembly gaps in BED format (can be downloaded from UCSC table browser) |
chrTable |
GRanges object of chromosome table (product of makeChrTable) |
verbose |
prints messages to the terminal (default is TRUE) |
overlapNum |
Minimal number of strand state changes that overlap with a gap before assembly is cut at that location |
a GRanges object of all contigs split by regions where the sceFile and gapFile GRanges objects overlap.