mapGapFromOverlap: mapGapFromOverlap - function to co-localize strand state...

In oneillkza/ContiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description

mapGapFromOverlap – function to co-localize strand state changes with assembly gaps

Usage

mapGapFromOverlap(sceFile, gapFile, chrTable, verbose = TRUE,
  overlapNum = 4)

Arguments

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

Value

a GRanges object of all contigs split by regions where the sceFile and gapFile GRanges objects overlap.

oneillkza/ContiBAIT documentation built on June 1, 2020, 5:49 a.m.