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, broman@wisc.edu

### 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)

[Package qtl version 1.46-2 Index]