mppR: IBS.mppData – R documentation

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IBS.mppData

IBS coding for mppData objects

Description

Transform the genotype marker matrix of a mppData object into Identical by state (IBS) 0, 1, 2 format. The IBS score represent the number of copies of the minor allele.

Usage

IBS.mppData(mppData)

Arguments

mppData

An object of class mppData. The mppData must have been processed using: create.mppData and QC.mppData.

Value

an increased mppData object containing the the same elements as the mppData object provided as argument and the following new elements:

`geno.IBS`	Marker `matrix` with marker scores coded as 0, 1, 2 corresponding to the number of copies of the least frequent SNP allele.
`allele.ref`	`matrix` with reference allele scores. The first row represents the minor allele (lowest frequency), the second the one represent the major allele (largest frequency) and the two others the heterozygous scores.

Author(s)

Vincent Garin

Examples

data(mppData_init)

mppData <- QC.mppData(mppData_init)

mppData <- IBS.mppData(mppData = mppData)

mppR

Multi-Parent Population QTL Analysis

v1.2.1

GPL-3

Authors

Vincent Garin [aut, cre], Valentin Wimmer [aut], Dietrich Borchardt [ctb, dtc], Fred van Eeuwijk [ctb, ths], Marcos Malosetti [ctb, ths]

Initial release

2020-02-10