oligo (version 1.36.1)

crlmm: Genotype Calls

Description

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

Usage

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())

Arguments

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.

Value

• SnpCallSetPlus object.