crlmm {oligo} | R Documentation |
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. |
SnpCallSetPlus
object.
## crlmmResults <- justCRLMM(list.celfiles())