BAIT {contiBAIT} | R Documentation |
BAIT – master function to process strand-seq libraries into BAIT ideograms
BAIT(path = ".", splitBy = 2e+05, readQual = 10, pairedEnd = TRUE, plotBy = "lib", plotName = NULL, chroms = "all", verbose = TRUE)
path |
String denoting location of Strand-seq bam files (default is ".") |
splitBy |
numeric value of binsize for plotting. default is 200000 |
readQual |
Integer dictating the minimal mapping quality required for a read to be accepted. Default is 10. |
pairedEnd |
Whether the bam files being read are in paired end format. Default is TRUE. Note, |
plotBy |
Whether to plot by library ('lib') or chromosome ('chr') |
plotName |
character which determines file name to be saved. Default is to open an R plot from the terminal |
chroms |
vector of chromosome number to prevent contig plotting. eg for humans use 1:24. Default is 'all' |
verbose |
prints messages to the terminal (default is TRUE) |
ideogram plots
## Not run: #Not run because this takes a minute or two: bamPath=file.path(system.file(package='contiBAIT'), 'extdata') BAIT(bamPath, pairedEnd = FALSE) #our example data is single-end ## End(Not run)