crlmm {oligo} | R Documentation

## 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.

[Package oligo version 1.52.1 Index]