hap.collapse: Merge duplicate individuals.

In trife/gbs: Tools for Genotyping-By-Sequencing Data

Description

Combines multiple individuals that have the same name (e.g. ind.1,ind.2,...,ind.n) in a gbs object.

Usage

hap.collapse(hap, names, match, het = "H")

Arguments

hap	A gbs object consisting only of individuals (columns) and markers (rows).
names	A list of the base names of the individual(s) to merge.
match	The percent matching individuals must be before merging.
het	The symbol(s) used for heterozygous calls.

Details

This function merges the calls from duplicate individuals. If a call for a given marker does not match between individuals, it is called heterozygous. All heterozygous markers are stored as "H".

Value

A gbs object with duplicate individuals merged.

Author(s)

Trevor Rife, [e-mail]

Examples

data(dh)
dh = hap.collapse(dh,names=c("TIGER","DANBY"),match=0.9)
head(dh$calls)

trife/gbs documentation built on May 31, 2019, 7:53 p.m.