predict.f1: Predict genotype of an F1 individual given genotypes of its...

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Predict genotype of an F1 individual given genotypes of its parents

Usage

## S3 method for class 'f1'
predict(object, na.rm = FALSE, ...)

Arguments

object	a genotypes object
na.rm	logical; should missing genotypes be ignored?
...	ignored

Details

Each column in the input is assumed to be either a representative individual from an inbred line, or a consensus genotype across several such individuals. No checks are performed on the homzygosity of the parents, but parents with high heterozygosity will result in F1 predictions with mostly missing genotypes.

When na.rm = TRUE, a missing genotype in either parent causes an NA to be emitted for the F1; when na.rm = FALSE, the non-missing parental genotype (if any) is emitted. Heterozygous calls in either parent always generate an NA in the F1.

F1s are named like "parent1::parent2".

Sex chromosomes and mitochonria receive no special treatment, so genotypes there will probably be bogus (except for the case of chrX in F1 females.)

Value

a new genotypes object containing predicted genotypes for all possible F1s between the parents in object

See Also

segregating, fixed.diffs

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.