correctGC {AneuFinder} | R Documentation |
Correct a list of binned.data
by GC content.
correctGC(binned.data.list, GC.BSgenome, same.binsize = FALSE, method = "loess", return.plot = FALSE, bins = NULL)
binned.data.list |
A |
GC.BSgenome |
A |
same.binsize |
If |
method |
One of |
return.plot |
Set to |
bins |
A |
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) }