writeBed: function to write contig order to BED file

Description Usage Arguments Value Examples

Description

function to write contig order to BED file

Usage

1
2
3
## 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

1
2
3
4
5
6
7
8
9
## Not run: 

data("exampleDividedChr")

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

## End(Not run)

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