replaceqtl: Replace a QTL in a qtl object with a different position

In kbroman/qtl: Tools for Analyzing QTL Experiments

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, [e-mail]

See Also

makeqtl, fitqtl, dropfromqtl, addtoqtl, reorderqtl

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)

kbroman/qtl documentation built on Aug. 26, 2024, 12:33 a.m.