writeBed,ANY,ChrTable,ContigOrdering-method {contiBAIT} | R Documentation |
function to write contig order to BED file
## S4 method for signature 'ANY,ChrTable,ContigOrdering' writeBed(chrTable, orientationData, contigOrder, libWeight = NULL, file = "contiBAIT_assembly.bed")
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 |
NULL; BED file written to file
## Not run: data("exampleDividedChr") writeBed(exampleDividedChr, reorientedMatrix[[2]], contigOrder) ## End(Not run)