writeBed,ANY,ChrTable,ContigOrdering-method {contiBAIT} | R Documentation

## function to write contig order to BED file

### 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)

[Package contiBAIT version 1.12.0 Index]