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, minPforCalls = c(.5, .1, .5), verbose = TRUE, correctionFile = NULL)

Arguments

object SnpQSet object
correction The output of the EM algorithm
recalibrate Logical - should recalibration be performed?
minPforCalls Minimum thresholds for genotype calls.
verbose Logical.
correctionFile A filename.

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.

Value

SnpCallSet object.

Note

Author(s)

References

See Also

Examples






[Package oligo version 1.0.2-6 Index]