mppR (version 1.2.1)

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.

See Also

create.mppData, QC.mppData

Examples

# NOT RUN {
data(mppData_init)

mppData <- QC.mppData(mppData_init)

mppData <- IBS.mppData(mppData = mppData)
      

# }