hss: Half-sib Family Splitter

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

Description

Splits the dataset into half-sib family groups based on a pedigree.

Usage

hss(pedigree, genotype, check = TRUE)

Arguments

pedigree	matrix the pedigree matrix should contain at least two columns, the first column with the half-sib IDs and the second column with the sires IDs
genotype	matrix genotype matrix with SNP ordered by mapping position in the columns. Data should be numeric. Use 0, 1 and 2 respectively for AA, AB and BB. Use 9 for missing data
check	logical check the genotype file for the possible errors

Details

Only half-sib groups that have more than 3 individuals will be returned.

Value

Returns a list of numeric matrices, each matrix is a half-sib family.

Note

Pedigree must have at least two columns with sample ids (Column 1) and sire ids (Column 2).

Examples

# Please run demo(hsphase)

Example output

Loading required package: snowfall
Loading required package: snow

hsphase documentation built on May 2, 2019, 3:44 p.m.