updateJoinMap: JoinMap format

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

JoinMap format

Description

The JoinMap software needs a locus genotype file ("loc-file") containing the information (genotypes, phased or not) of the loci for a single segregating population. This function converts a data.frame in the JoinMap v2 format into the JoinMap v3-v4 format. It is assumed that the population is of type CP: "a population resulting from a cross between two heterogeneously heterozygous and homozygous diploid parents, linkage phases originally (possibly) unknown".

Usage

updateJoinMap(x, verbose = 1)

Arguments

x	data.frame in the JoinMap v2 format; the first four lines of a JoinMap loc-file should be absent; columns <locus name>, [PHASE] and [CLAS] are ignored; missing genotypes are coded as "–"
verbose	verbosity level (0/1)

Value

data.frame

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.