makeChrTable {contiBAIT} | R Documentation |
makeChrTable – Pulls out chromosome and length data from the header of a bam file
makeChrTable(bamFile, splitFile = NULL, splitBy = NULL, verbose = TRUE)
bamFile |
string of location of a bam file to extract header data from |
splitFile |
GRanges object (of type chr, start and end: no strand or meta columns) of locations in which to split the assembly, such as previously determined locations of contig chimerism |
splitBy |
integer determining the average size contigs should be split by |
verbose |
if FALSE, no messages appear on terminal |
makeChrTable creates a table with chromosome name and chromosome length by extracting header data from the supplied bam file.
a GRanges object of class ChrTable, containing information on the organism's chromosomes as extracted from the BAM file header.
#Get an example BAM file and generate a chromosome table featuring fragment names and lengths example.bam <- list.files(file.path(system.file(package='contiBAIT'), 'extdata'), full.names=TRUE)[1] chrTable <- makeChrTable(example.bam) show(chrTable) dividedChr <- makeChrTable(example.bam, splitBy=1000000) show(dividedChr)