writeBed: function to write contig order to BED file

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

Description

function to write contig order to BED file

Usage

## S4 method for signature 'ANY,ChrTable,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	ChrTable of contig and strand (with rownames matching contig names). Product of reorientAndMergeLGs[[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

## Not run: 

data("exampleDividedChr")

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

## End(Not run)

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