qtl: pull.argmaxgeno – R documentation

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qtl

pull.argmaxgeno

Pull out the results of the Viterbi algorithm from a cross

Description

Pull out the results of argmax.geno from a cross as a matrix.

Usage

pull.argmaxgeno(cross, chr, include.pos.info=FALSE, rotate=FALSE)

Arguments

`cross`	An object of class `cross`. See `read.cross` for details.
`chr`	Optional vector indicating the chromosomes to consider. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
`include.pos.info`	If TRUE, include columns with marker name, chromosmoe ID, and cM position. (If `include.pos.info=TRUE`, we take `rotate=TRUE`.)
`rotate`	If TRUE, return matrix with individuals as columns and positions as rows. If FALSE, rows correspond to individuals.

Value

A matrix containing numeric indicators of the inferred genotypes. Multiple chromosomes are pasted together.

Author(s)

Karl W Broman, broman@wisc.edu

Examples

data(listeria)
listeria <- argmax.geno(listeria, step=1, stepwidth="max")
amg <- pull.argmaxgeno(listeria, chr=c(5,13), include.pos.info=TRUE, rotate=TRUE)
amg[1:5,1:10]

qtl

Tools for Analyzing QTL Experiments

v1.48-1

GPL-3

Authors

Karl W Broman <broman@wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, Brian Yandell, and R Core Team

Initial release

2021-03-24