associateGenotypes {SNPhood} | R Documentation

## Associate genotypes with user regions from a SNPhood object.

### Description

The function `associateGenotypes` associates genotypes with SNP regions as defined in a `SNPhood` object. It is possible to assign genotypes only for a subset of datasets as defined in a `SNPhood` object. To avoid any ambiguities, a 1:1 for genotype and dataset mapping must be given (ses below).

### Usage

    associateGenotypes(SNPhood.o, genotypeMapping, verbose = TRUE)

### Arguments

`SNPhood.o` | Object of class `SNPhood`
`genotypeMapping` | Data frame. A data frame that establishes the mapping between datasets in the object and the corresponding genotype file and column names. See the examples. must be provided. See the Vignette for a more detailed description of the supported file format.
`verbose` | Logical(1). Default TRUE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

### Value

Object of class `SNPhood` with the genotype information added to the slot `annotation`, element genotype. You may retrieve it via the accessor function `annotation`.

### Examples

    data(SNPhood.o, package="SNPhood")
    fileGenotypes = list.files(pattern = "*genotypes*",system.file("extdata", package = "SNPhoodData"), full.names = TRUE)
    mapping = data.frame(samples = annotationDatasets(SNPhood.o), genotypeFile = rep(fileGenotypes, 2), sampleName = c("NA10847", "NA12890"))
    SNPhood.o = associateGenotypes(SNPhood.o, mapping)

[Package SNPhood version 1.16.0 Index]