setupGADA.B.deviation: Imports array data to MAD
In isglobal-brge/MAD: Mosaic Alteration Detector(MAD)

Description Usage Arguments

Imports array data to MAD

setupGADA.B.deviation(file, NumCols, GenoCol, log2ratioCol, BAFcol,
  name.geno = c("AA", "AB", "BB"), chrs = c(1:22, "X", "Y"),
  MarkerIdCol = 1, ChrNameCol = 2, ChrPosCol = 3, sort = TRUE,
  orderProbes, sep = "\t", saveGenInfo = TRUE)

`file`	A pennCNV-style file
`NumCols`	The number of columns in 'file'
`GenoCol`	The column in 'file' containing genotypes
`log2ratioCol`	The column in 'file' containing log2ratio intensities
`name.geno`	the name of the genotypes (default "AA", "AB" and "BB)
`chrs`	The names of the chromosomes. Default 1, ..., 22, X, Y
`MarkerIdCol`	The column in 'file' containing the name of the marker. Default first column
`ChrNameCol`	The column in 'file' containing the chromosome. Default second column
`ChrPosCol`	The column in 'file' containing the genomic position. Default third column
`sort`	should data be sorted by genomic position? The default is TRUE.
`orderProbes`	used to avoid sorting
`sep`	how data columns are separated. Default by tab
`saveGenInfo`	Should annotation data be saved? The default is TRUE. See details
`BAFCol`	The column in 'file' containing B-allele frequency (BAF)