crlmm {oligo}R Documentation

Genotype Calls

Description

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

Usage

crlmm(object, correction = NULL, recalibrate = TRUE, minLLRforCalls =
c(5, 1, 5), verbose = TRUE,  correctionFile = NULL, prefix =
"tmp.crlmm.", balance = 1.5)
justCRLMM(filenames, batch_size = 40000, minLLRforCalls = c(5, 1, 5),
recalibrate = TRUE, balance = 1.5, phenoData = NULL, verbose = TRUE,
pkgname = NULL)

Arguments

object SnpQSet object
filenames character vector with the filenames.
batch_size integer defining how many SNPs should be processed at a time.
correction The output of the EM algorithm
recalibrate Logical - should recalibration be performed?
prefix String defining the prefix to be used with the temporary files.
balance Control parameter to balance homozygotes and heterozygotes calls.
minLLRforCalls Minimum thresholds for genotype calls.
verbose Logical.
correctionFile A filename.
phenoData phenoData object or NULL
pkgname alt. pdInfo package to be used

Details

The correctionFile is a string (eg, "outputEM.rda") pointing to a filename. If the file does not exist, crlmm will save a file with that name containing the results of the EM algorithm. If the file exists, its content is loaded and used by CRLMM. The correctionFile is meant to save time if crlmm is be run multiple times, as the EM algorithm does not need to be run everytime.

The justCRLMM method is more efficient in terms of memory. It uses the CEL files directly, taking SNPs by batch.

Value

SnpCallSetPlus object.

Note

Author(s)

References

See Also

Examples

## crlmmResults <- justCRLMM(list.celfiles())

[Package oligo version 1.2.2 Index]