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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/makeqtl.R

Description

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

Usage

1
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

See Also

makeqtl, fitqtl, dropfromqtl, addtoqtl, reorderqtl

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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 documentation built on June 20, 2017, 9:05 a.m.

Search within the qtl package
Search all R packages, documentation and source code