genotypeAffy {crlmm} | R Documentation

## Genotype Affymetrix CEL files

### Description

Assign diallelic genotypes at polymorphic markers

### Usage

    genotypeAffy(cnSet, SNRMin = 5, recallMin = 10, recallRegMin = 1000, gender = NULL, badSNP = 0.7, returnParams = TRUE, verbose = TRUE)

### Arguments

`cnSet` | An object of class `CNSet`
`SNRMin` | See `crlmm`
`recallMin` | See `crlmm`
`recallRegMin` | See `crlmm`
`gender` | See `crlmm`
`badSNP` | See `crlmm`
`returnParams` | See `crlmm`
`verbose` | Logical.

### Details

Wrapper for crlmm genotyping.

### Value

Returns logical. SNP genotypes and confidence scores are written to `ff_matrix` objects.

### Author(s)

R.Scharpf

### See Also

`crlmm`, `calls`, `confs`

[Package crlmm version 1.45.0 Index]