WES.Normalize: Normalization of binned WES data.
In gustaveroussy/EaCoN: EaCoN : Easy Copy Number !

Description Usage Arguments Value Author(s)

This function performs the normalization of the L2R and BAF signals from a data object obtained with WES.Bin() (or WES.Bin.Batch()).

WES.Normalize(data = NULL, BINpack = NULL, gc.renorm = TRUE,
wave.renorm = FALSE, wave.rda = NULL, RD.tot.min = 20, RD.alt.min = 3,
BAF.hetmin = .33, sex.chr = c("chrX", "chrY"), TumorBoost = FALSE,
out.dir = getwd(), return.data = FALSE, write.data = TRUE, plot = TRUE)

`data`	Data object contained in a RDS file generated with `EaCoN.WES.Bin()`.
`BINpack`	A data pack generated with `EaCoN.BINpack.Maker()` containing to a binned version of the capture BED used to generate the BAM files, and corresponding precomputed GC% tracks.
`gc.renorm`	Perform a 'GC-content' normalization of read depth.
`wave.renorm`	Perform a 'Wave-effect' normalization of read depth.
`wave.rda`	If `wave.norm` set to `TRUE`, specifies the data package containing Wave tracks.
`RD.tot.min`	Minimum total read depth in the test and REF BAMs to keep a log2(ratio) bin.
`RD.alt.min`	Minimum alternate nucleotide read depth in the test BAM to keep a SNP position.
`BAF.hetmin`	BAF threshold for reference to consider a SNP position as heterozygous.
`sex.chr`	Name of the gonosomes. Please verify that provided name(s) is (are) compatible with chromosome names used in the corresponding BSgenome package (if none, use `NULL`).
`TumorBoost`	Perform a normalization of the Test BAF profile using the Ref BAF profile, thanks to the TumorBoost methods (see `?aroma.light::normalizeTumorBoost())`).
`out.dir`	Output directory.
`return.data`	Return the results.
`write.data`	Write the results as a RDS file.
`plot`	Perform plots.