correctGC: GC correction
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description Usage Arguments Details Value Author(s) Examples

Correct a list of binned.data by GC content.

1 2	correctGC(binned.data.list, GC.BSgenome, same.binsize = FALSE, method = "loess", return.plot = FALSE, bins = NULL)

`binned.data.list`	A `list` with `binned.data` objects or a list of filenames containing such objects.
`GC.BSgenome`	A `BSgenome` object which contains the DNA sequence that is used for the GC correction.
`same.binsize`	If `TRUE` the GC content will only be calculated once. Set this to `TRUE` if all `binned.data` objects describe the same genome at the same binsize and stepsize.
`method`	One of `c('quadratic', 'loess')`. Option `method='quadratic'` uses the method described in the Supplementary of `citation("AneuFinder")`. Option `method='loess'` uses a loess fit to adjust the read count.
`return.plot`	Set to `TRUE` if plots should be returned for visual assessment of the GC correction.
`bins`	A `binned.data` object with meta-data column 'GC'. If this is specified, `GC.BSgenome` is ignored. Beware, no format checking is done.

Two methods are available for GC correction: Option method='quadratic' uses the method described in the Supplementary of citation("AneuFinder"). Option method='loess' uses a loess fit to adjust the read count.

A list() with binned.data objects with adjusted read counts. Alternatively a list() with ggplot objects if return.plot=TRUE.

Aaron Taudt

## Get a BED file, bin it and run GC correction
bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData")
binned <- binReads(bedfile, assembly='mm10', binsize=1e6,
                  chromosomes=c(1:19,'X','Y'))
plot(binned[[1]], type=1)
if (require(BSgenome.Mmusculus.UCSC.mm10)) {
 binned.GC <- correctGC(list(binned[[1]]), GC.BSgenome=BSgenome.Mmusculus.UCSC.mm10)
 plot(binned.GC[[1]], type=1)
}