processBdevMAD: Process MAD file to obtain Bdev

In isglobal-brge/MADloy: Package to detect mosaic LOY from SNP array data

Process MAD file to obtain Bdev

Description

Process a MAD file to retrieve the B deviation in a region of interest.

Usage

processBdevMAD(
  file,
  regions,
  rsCol,
  ChrCol,
  PosCol,
  LRRCol,
  BAFCol,
  top,
  bot,
  trim
)

Arguments

file	File path of the MAD file to be processed.
regions	Regions of chromosomes X and Y in data.frame. See system.file("extdata", "references") for more info on these regions.
rsCol	Column of the MAD file with the name of the SNP.
ChrCol	Column of the MAD file with the chromosome information.
PosCol	Column of the MAD file with the position information.
LRRCol	Column of the MAD file with the Log R Ratio information.
BAFCol	Column of the MAD file with the B Allele Frequency information.
top	Superior treshold to consider an heterozygous allele.
bot	Inferior treshold to consider an heterozygous allele.
trim	the fraction (0 to 0.5) of probes to be trimmed when summaryzing LRR. This argument tries to control the effect of having CNVs in the analyzed region. Default is 0.1.

Value

A list with the Bdev for the query value.

Examples

## Not run: 
processBdevMAD(file=file.path, query=rangedDataROI, rsCol=1, chrCol=2, PosCol=3, LRRCol=4)
## End(Not run)

isglobal-brge/MADloy documentation built on March 3, 2024, 7:27 p.m.