BINpack.Maker: Generates a "BINpack" containing binned data and GC tracks...
In gustaveroussy/EaCoN: EaCoN : Easy Copy Number !

Description Usage Arguments Details Value Author(s)

This function performs the binning of WES data from a BED of the captured regions and compute corresponding GC% with optional elongation.

BINpack.Maker(bed.file = NULL, bin.size = 50, genome.pkg =
"BSgenome.Hsapiens.UCSC.hg19", extend.multi = c(0, 50, 100, 200, 400, 800,
1600, 3200, 6400), blocksize = 1E+04, nthread = 1, out.dir = getwd(),
return.data = FALSE)

`bed.file`	BED File corresponding to the captured genomic regions in the WES experiment (usually given by the manufacturer.
`bin.size`	Size of the bins (in nucleotides) to reduce WES data.
`genome.pkg`	Name of the BSgenome package corresponding to the genome used to map the BAM files.
`extend.multi`	Vector of integers corresponding to lengths to extend (on both sides) the BED regions to compute GC%.
`blocksize`	Size (in lines) of the block of BED regions to compute GC% in multithreading mode (to limit RAM consumption).
`nthread`	Number of thread(s).
`out.dir`	Output directory.
`return.data`	Return the results.

Before BED slicing in bins of specified size and GC% computations, a cleaning of the BED is automaticaly performed, to fix some possible BED errors (inversed coordinates, duplicated or overlapping intervals, etc).

A data pack (.rda) corresponding to the binned BED of captured regions with its precomputed GC%. If return.data is set to TRUE, its content is also returned.

Bastien Job

gustaveroussy/EaCoN documentation built on Oct. 20, 2021, 2:41 a.m.