qtl: subset.scanone – R documentation

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qtl

subset.scanone

Subsetting the results of a genome scan

Description

Pull out a specified set of chromosomes and/or LOD columns from scanone output.

Usage

## S3 method for class 'scanone'
subset(x, chr, lodcolumn, ...)

Arguments

`x`	An object of class `scanone`, output from `scanone`.
`chr`	Optional vector specifying which chromosomes to keep. 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.
`lodcolumn`	A vector specifying which LOD columns to keep (or, if negative), omit. These should be between 1 and the number of LOD columns in the input `x`.
`...`	Ignored at this point.

Value

The input scanone object, but with only the specified subset of the data.

Author(s)

Karl W Broman, broman@wisc.edu

Examples

data(fake.bc)

fake.bc <- calc.genoprob(fake.bc, step=2.5)
out <- scanone(fake.bc, method="hk", pheno.col=1:2)

summary(subset(out, chr=18:19), format="allpeaks")

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