createBins: Builds bin annotation data for a particular bin size

In ccagc/QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

Builds bin annotation data for a particular bin size

Description

Builds bin annotation data for a particular bin size.

Usage

createBins(bsgenome, binSize, ignoreMitochondria=TRUE, excludeSeqnames=NULL,
  verbose=getOption("QDNAseq::verbose", TRUE))

Arguments

bsgenome	A BSgenome package.
binSize	A numeric scalar specifying the width of the bins in units of kbp (1000 base pairs), e.g. binSize=15 corresponds to 15 kbp bins.
ignoreMitochondria	Whether to ignore the mitochondria, defined as chromosomes named 'chrM', 'chrMT', 'M', or 'MT'.
excludeSeqnames	Character vector of seqnames which should be ignored.
verbose	If TRUE, verbose messages are produced.

Value

Returns a data.frame with columns chromosome, start, end, bases, and gc, which correspond to the chromosome name, positions of the first and last base pair in the bin, the percentage of characterized nucleotides (A, C, G, or T, i.e. non-N), and GC content (percentage of C and G nucleotides of non-N nucleotides).

Parallel processing

The future is used parallelize the following functions:

• createBins() - parallelizes binned GC content across chromosomes

• calculateBlacklist() - parallelizes overlap counts across bins)

Author(s)

Ilari Scheinin

See Also

getBinAnnotations().

Examples

## Not run: # NOTE: These take a very long time to run.
library(BSgenome.Hsapiens.UCSC.hg19)
bins <- createBins(BSgenome.Hsapiens.UCSC.hg19, 15)
bins$mappability <- calculateMappability(bins,
    bigWigFile='/path/to/wgEncodeCrgMapabilityAlign50mer.bigWig',
    bigWigAverageOverBed='/path/to/bigWigAverageOverBed')
bins$blacklist <- calculateBlacklist(bins,
    bedFiles=c('/path/to/wgEncodeDacMapabilityConsensusExcludable.bed',
    '/path/to/wgEncodeDukeMapabilityRegionsExcludable.bed'))
bins$residual <- iterateResiduals(readCountsG1K)

## End(Not run)

ccagc/QDNAseq documentation built on Feb. 2, 2023, 12:56 p.m.