qtl: subset.scanoneperm – R documentation

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qtl

subset.scanoneperm

Subsetting permutation test results

Description

Pull out results for a specified set LOD columns from permutation results from scanone.

Usage

## S3 method for class 'scanoneperm'
subset(x, repl, lodcolumn, ...)
## S3 method for class 'scanoneperm'
x[repl, lodcolumn]

Arguments

`x`	Permutation results from `scanone`, run with `n.perm`>0.
`repl`	A vector specifying which permutation replicates to keep or (if negative) omit.
`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 permutation results, 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=5)
operm <- scanone(fake.bc, method="hk", pheno.col=1:2, n.perm=25)
operm2 <- subset(operm, lodcolumn=2)

# alternatively
operm2alt <- operm[,2]

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