genotypeInf {crlmm} | R Documentation

## Genotyping of Illumina Infinium II arrays.

### Description

Genotyping of Illumina Infinium II arrays. This function provides CRLMM/KRLMM genotypes and confidence scores for the the polymorphic markers and is a required step prior to copy number estimation.

### Usage

    genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5,
                 recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams = TRUE,
                 badSNP = 0.7, gender = NULL, DF = 6, cdfName, nopackage.norm="quantile",
                 call.method="crlmm", trueCalls = NULL)

### Arguments

`cnSet` | An object of class `CNSet`
`mixtureParams` | `data.frame` containing mixture model parameters needed for genotyping. The mixture model parameters are estimated from the `preprocessInf` function.
`probs` | 'numeric' vector with priors for AA, AB and BB.
`SNRMin` | 'numeric' scalar defining the minimum SNR used to filter out samples.
`recallMin` | Minimum number of samples for recalibration.
`recallRegMin` | Minimum number of SNP's for regression.
`verbose` | 'logical.' Whether to print descriptive messages during processing.
`returnParams` | 'logical'. Return recalibrated parameters from crlmm.
`badSNP` | 'numeric'. Threshold to flag as bad SNP (affects batchQC)
`gender` | integer vector ( male = 1, female =2 ) or missing, with same length as filenames. If missing, the gender is predicted.
`DF` | 'integer' with number of degrees of freedom to use with t-distribution.
`cdfName` | `character` string indicating which annotation package to load.
`nopackage.norm` | character string specifying normalization to be used when `cdfName`='nopackage'. Options are 'none', 'quantile' (within channel, between array) and 'quantileloess'.
`call.method` | character string specifying the genotype calling algorithm to use ('crlmm' or 'krlmm').
`trueCalls` | matrix specifying known Genotype calls for a subset of samples and features(1 - AA, 2 - AB, 3 - BB).

### Details

The genotype calls and confidence scores are written to file using `ff` protocols for I/O. For the most part, the calls and confidence scores can be accessed as though the data is in memory through the methods `snpCall` and `snpCallProbability`, respectively.

The genotype calls are stored using an integer representation: 1 - AA, 2 - AB, 3 - BB. Similarly, the call probabilities are stored using an integer representation to reduce file size using the transformation 'round(-1000*log2(1-p))', where p is the probability. The function `i2P` can be used to convert the integers back to the scale of probabilities.

An optional `trueCalls` argument can be provided to KRLMM method which contains known genotype calls(can contain some NAs) for some samples and SNPs. This will used to compute KRLMM parameters by calling `vglm` function from `VGAM` package.

The KRLMM method makes use of functions provided in `parallel` package to speed up the process. It by default initialises up to 8 clusters. This is configurable by setting up an option named "krlmm.cores", e.g. options("krlmm.cores" = 16).

### Value

Logical. If the genotyping is completed, the value 'TRUE' is returned. Note that `assayData` elements 'call' and 'callProbability' are updated on disk. Therefore, the genotypes and confidence scores can be retrieved using accessors for the `CNSet` class.

### Author(s)

R. Scharpf

### See Also

`crlmm`, `snpCall`, `snpCallProbability`, `annotationPackages`

### Examples

    	## See the 'illumina_copynumber' vignette in inst/scripts of
    	## the source package

[Package crlmm version 1.48.0 Index]