crlmm {oligo} | R Documentation |
Performs genotype calls via CRLMM (Corrected Robust Linear Model with Maximum-likelihood based distances).
crlmm(object, correction = NULL, recalibrate = TRUE, minPforCalls = c(.5, .1, .5), verbose = TRUE, correctionFile = NULL)
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. |
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.
SnpCallSet
object.