blacklist: Make a blacklist for genomic regions
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description Usage Arguments Value Examples

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.

1	blacklist(files, assembly, bins, min.mapq = 10, pairedEndReads = FALSE)

`files`	A character vector of either BAM or BED files.
`assembly`	Please see `fetchExtendedChromInfoFromUCSC` for available assemblies. Only necessary when importing BED files. BAM files are handled automatically. Alternatively a data.frame with columns 'chromosome' and 'length'.
`bins`	A list with one `GRanges-class` with binned read counts generated by `fixedWidthBins`.
`min.mapq`	Minimum mapping quality when importing from BAM files. Set `min.mapq=NA` to keep all reads.
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your BAM files (not implemented for BED files).

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]