setupQtlCrossObject: Set-up a R/qtl "cross" object

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

Set-up a R/qtl "cross" object

Description

Set up a "cross" object from the qtl package.

Usage

setupQtlCrossObject(gendat, cross.type, genmap = NULL, phenos = NULL)

Arguments

gendat	genotype data in the qtl format as a matrix with genotypes in rows and markers in columns; if genmap is provided, only the markers also on the map will be kept
cross.type	type of cross ("bc" for a backcross, "4way" for a cross between two outbred parents)
genmap	genetic map as a data frame with one row per marker and at least two columns named "linkage.group" and "locus"; if a third one, "genetic.distance", is absent, it will be created and filled with fake, incremental values; if NULL, a fake genetic map will be created with all markers in the same linkage group; it is assumed that all linkage groups correspond to autosomes
phenos	data frame containing the phenotypes; if not NULL, the genotype identifiers should be in a column named "Genotype" or as row names; otherwise, will be created with such a column

Value

object of class "cross" as defined in the qtl package

Author(s)

Timothee Flutre

See Also

joinMap2backcross

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