mapGapFromOverlap {contiBAIT} | R Documentation

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

### 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.

[Package contiBAIT version 1.14.0 Index]