imputationData: Get out the IBD genotype imputation data

In mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description

Get out the IBD genotype imputation data

Usage

imputationData(object, ...)

## S4 method for signature 'imputed'
imputationData(object, ...)

## S4 method for signature 'geneticData'
imputationData(object, ...)

## S4 method for signature 'mpcrossMapped'
imputationData(object, ...)

Arguments

object	The object from which to extract the IBD genotype imputation data
...	Extra parameters. Currently only "experiment" is supported, letting the user extract the imputation data for a specific experiment.

Details

Extract the IBD genotype imputation data. The data takes the form of a matrix of values, with rows corresponding to genetic lines and columns corresponding to genetic positions. The genetic positions may include non-marker positions, so use imputationMap to find out the chromosome and position for every marker.

Each value in the matrix represents the predicted genotype for that genetic line, at that position. In the case of completely inbred experiments, each value in the matrix represents the founders from which that allele is believed to be derived. In the case of experiments with residual heterozygosity, the possible genotypes include heterozygotes, and the interpretation of the values in the matrix is more complicated. Function imputationKey gives information about how the values in the matrix correspond to actual genotypes.

Value

The IBD genotype imputation data.

mpMap2 documentation built on Sept. 13, 2020, 5:17 p.m.