blacklist {AneuFinder} | R Documentation |
Produce a blacklist of genomic regions with a high ratio of duplicate to unique reads. This blacklist can be used to exclude reads for analysis in Aneufinder
, bam2GRanges
and bed2GRanges
. This function produces a pre-blacklist which has to manually be filtered with a sensible cutoff. See the examples section for details.
blacklist(files, assembly, bins, min.mapq = 10, pairedEndReads = FALSE)
files |
A character vector of either BAM or BED files. |
assembly |
Please see |
bins |
A list with one |
min.mapq |
Minimum mapping quality when importing from BAM files. Set |
pairedEndReads |
Set to |
A GRanges-class
with the same coordinates as bins
with metadata columns ratio, duplicated counts and deduplicated counts.
## Get an example BAM file with single-cell-sequencing reads bamfile <- system.file("extdata", "BB150803_IV_074.bam", package="AneuFinderData") ## Prepare the blacklist bins <- fixedWidthBins(assembly='mm10', binsizes=1e6, chromosome.format='NCBI') pre.blacklist <- blacklist(bamfile, bins=bins) ## Plot a histogram to decide on a sensible cutoff qplot(pre.blacklist$ratio, binwidth=0.1) ## Make the blacklist with cutoff = 1.9 blacklist <- pre.blacklist[pre.blacklist$ratio > 1.9]