blacklist {AneuFinder} | R Documentation

## Make a blacklist for genomic regions

### Description

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.

### Usage

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

### Arguments

`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).

### Value

A `GRanges-class` with the same coordinates as `bins` with metadata columns ratio, duplicated counts and deduplicated counts.

### Examples

    ## 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]

[Package AneuFinder version 1.8.0 Index]