processBdevMAD: Process MAD file to obtain Bdev

Description Usage Arguments Value Examples

View source: R/processBdevMAD.R

Description

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

Usage

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

Arguments

file

File path of the MAD file to be processed.

query

Region of interest to check the LRR in rangedData format.

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

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## 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 June 11, 2017, 2:40 a.m.