imputation.cmbgeno: Impute genotypes of F2 populations based on flanking markers.

In lian0090/F2imputation: Impute F2 populations

Description

Impute genotypes of F2 populations based on flanking markers. The input format should be combinedgeno.

Usage

imputation(combinedgeno)

Arguments

combinedgeno

nmar+1 columns and nLINE+4 rows. First column is LINE names, first four rows are map chr, map pos, P1 genotype and P2 genotype

Value

return out:a list of pimputedgeno and genoprob out$pimputedgeno is the same format as combinedgeno, but with the imputed geotypes out$genoprob an array of nLINE * nmar* 3. The probabilities of three gentoypes (-1,0,1)

Author(s)

Lian Lian

References

conditional expectation table for F2

Examples

data(combinedgeno)
outcmb=imputation.cmbgeno(combinedgeno)
outcmb.geno=outcmb$pimputedgeno[-c(1:4),]
outcmb.prob=outcmb$genoprob
data(progeno)
data(pargeno)
data(map)
out=imputation(progeno,pargeno,map,nColSkip=1,IDcol=NULL)
out.geno=out$pimputedgeno
out.prob=out$genoprob
all(out.geno==outcmb.geno)
all(out.prob==outcmb.prob)

lian0090/F2imputation documentation built on May 21, 2019, 6:09 a.m.