processMAD: Process MAD file

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

Process MAD file

Description

Process a MAD file to retrieve the median log R ratio of a region of interest.

Usage

processMAD(file, query, rsCol, ChrCol, PosCol, LRRCol, trim = 0.1)

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 LRR information.
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 across genome. Default is 0.1.

Value

A list with the mean of the LRR for the query value.

Examples

## Not run: 
    processMAD(file=file.path, query=rangedDataROI, rsCol=2, chrCol=3, PosCol=4, LRRCol=5)

## End(Not run)

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