qtl: replaceqtl – R documentation

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qtl

replaceqtl

Replace a QTL in a qtl object with a different position

Description

This function replaces a QTL or QTLs in a qtl object with a different position.

Usage

replaceqtl(cross, qtl, index, chr, pos, qtl.name, drop.lod.profile=TRUE)

Arguments

`cross`	An object of class `cross`. See `read.cross` for details.
`qtl`	A qtl object, as created by `makeqtl`.
`index`	Numeric index indicating the QTL to be replaced.
`chr`	Vector (of same length as `index`) indicating the chromosomes for the new QTL.
`pos`	Vector (of same length as `index`) indicating the positions for the new QTL. If there is no marker or pseudomarker at a position, the nearest position is used.
`qtl.name`	Optional vector (of same length as `index`) of user-specified names for each new QTL, used in the drop-one-term ANOVA table in `fitqtl`. If unspecified, the names will be of the form `"Chr1@10"` for a QTL on Chromsome 1 at 10 cM.
`drop.lod.profile`	If TRUE, remove any LOD profiles from the object.

Value

The input qtl object, but with some QTL replaced by new ones. See makeqtl for details on the format.

Author(s)

Karl W Broman, broman@wisc.edu

Examples

data(fake.f2)

# take out several QTLs and make QTL object
qc <- c(1, 6, 13)
qp <- c(25.8, 33.6, 18.63)
fake.f2 <- subset(fake.f2, chr=qc)

fake.f2 <- calc.genoprob(fake.f2, step=2, err=0.001)
qtl <- makeqtl(fake.f2, qc, qp, what="prob")

qtl <- replaceqtl(fake.f2, qtl, 2, 6, 48.1)

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