qtl: cbind.scanoneperm – R documentation

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qtl

cbind.scanoneperm

Combine columns from multiple scanone permutation results

Description

Concatenate the columns from different runs of scanone with n.perm > 0.

Usage

## S3 method for class 'scanoneperm'
cbind(..., labels)

Arguments

`...`	A set of objects of class `scanoneperm`. These are the permutation results from `scanone` (that is, when `n.perm > 0`), generally run with different phenotypes or methods.
`labels`	A vector of character strings, of length 1 or of the same length as the input `...`, to be appended to the column names in the output.

Details

The aim of this function is to concatenate the results from multiple runs of a permutation test scanone, generally for different phenotypes and/or methods, to be used in parallel with c.scanone.

Value

The concatenated input, as a scanoneperm object. If different numbers of permutation replicates were used, those columns with fewer replicates are padded with missing values (NA).

Author(s)

Karl W Broman, broman@wisc.edu

Examples

data(fake.f2)
fake.f2 <- calc.genoprob(fake.f2)

operm1 <- scanone(fake.f2, method="hk", n.perm=10, perm.Xsp=TRUE)
operm2 <- scanone(fake.f2, method="em", n.perm=5, perm.Xsp=TRUE)

operm <- cbind(operm1, operm2, labels=c("hk","em"))
summary(operm)

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