crlmm: Genotype Calls
In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays

Performs genotype calls via CRLMM (Corrected Robust Linear Model with Maximum-likelihood based distances).

crlmm(filenames, outdir, batch_size=40000, balance=1.5,
      minLLRforCalls=c(5, 1, 5), recalibrate=TRUE,
      verbose=TRUE, pkgname, reference=TRUE)
justCRLMM(filenames, batch_size = 40000, minLLRforCalls = c(5, 1, 5),
recalibrate = TRUE, balance = 1.5, phenoData = NULL, verbose = TRUE,
pkgname = NULL, tmpdir=tempdir())

`filenames`	character vector with the filenames.
`outdir`	directory where the output (and some tmp files) files will be saved.
`batch_size`	integer defining how many SNPs should be processed at a time.
`recalibrate`	Logical - should recalibration be performed?
`balance`	Control parameter to balance homozygotes and heterozygotes calls.
`minLLRforCalls`	Minimum thresholds for genotype calls.
`verbose`	Logical.
`phenoData`	`phenoData` object or `NULL`
`pkgname`	alt. pdInfo package to be used
`reference`	logical, defaulting to TRUE ...
`tmpdir`	Directory where temporary files are going to be stored at.