contiBAIT (version 1.0.0)

writeBed,ANY,OrientationFrame,ContigOrdering-method: function to write contig order to BED file

Description

function to write contig order to BED file

Usage

## S3 method for class 'ANY,OrientationFrame,ContigOrdering':
writeBed(chrTable,
  orientationData, contigOrder, libWeight = NULL,
  file = "contiBAIT_assembly.bed")

Arguments

chrTable

a GRanges object with a 'name' meta column matching contig names. Product of makeChrTable

orientationData

data.frame of contig and strand (with rownames matching contig names). Product of reorientLinkageGroups[[2]]

contigOrder

an object of type ContigOrdering with ordered Linkage Groups and contigs. Product of orderAllLinkageGroups

libWeight

average quality across all libraries for a contig

file

character string for bed file name to write

Value

• NULL; BED file written to file

Examples

data("exampleDividedChr")

writeBed(exampleDividedChr,
		 reorientedMatrix[[2]],
		 contigOrder)