function to write contig order to BED file

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Description

function to write contig order to BED file

Usage

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## S4 method for signature '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 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

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## Not run: 

data("exampleDividedChr")

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

## End(Not run)

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