qtl (version 1.66)

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)

Value

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

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.

Author

Karl W Broman,

See Also

pull.geno, pull.genoprob, pull.draws, argmax.geno

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]