R: Replace a QTL in a qtl object with a different position.

replaceqtl {qtl}

R Documentation

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, kbroman@biostat.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)

[Package qtl version 1.11-12 Index]