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

Description Usage Arguments Value

View source: R/mapGapFromOverlap.R

Description

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

Usage

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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.