R: Make a qtl object

makeqtl {qtl} | R Documentation

## Make a qtl object

### Description

This function takes a cross object and specified chromosome numbers and positions and pulls out the genotype probabilities or imputed genotypes at the nearest pseudomarkers, for later use by the function `fitqtl`.

### Usage

    makeqtl(cross, chr, pos, qtl.name, what=c("draws","prob"))

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`chr` | Vector indicating the chromosome for each QTL. (These should be character strings referring to the chromosomes by name.)
`pos` | Vector (of same length as `chr`) indicating the positions on the chromosome to be taken. If there is no marker or pseudomarker at a position, the nearest position is used.
`qtl.name` | Optional user-specified name for each 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.
`what` | Indicates whether to pull out the imputed genotypes or the genotype probabilities.

### Details

This function will take out the genotype probabilities and imputed genotypes if they are present in the input `cross` object. If both fields are missing in the input object, the function will report an error. Before running this function, the user must have first run either `sim.geno` (for `what="draws"`) or `calc.genoprob` (for `what="prob"`).

### Value

An object of class `qtl` with the following elements (though only one of `geno` and `prob` will be included, according to whether `what` is given as `"draws"` or `"prob"`):

``geno`` | Imputed genotypes.
``prob`` | Genotype probabilities.
``name`` | User-defined name for each QTL, or a name of the form `"Chr1@10"`.
``altname`` | QTL names of the form `"Q1"`, `"Q2"`, etc.
``chr`` | Input vector of chromosome numbers.
``pos`` | Input vector of chromosome positions.
``n.qtl`` | Number of QTLs.
``n.ind`` | Number of individuals.
``n.gen`` | A vector indicating the number of genotypes for each QTL.

### Author(s)

Hao Wu; Karl W Broman, broman@wisc.edu

### See Also

`fitqtl`, `calc.genoprob`, `sim.geno`, `dropfromqtl`, `replaceqtl`, `addtoqtl`, `summary.qtl`, `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 <- sim.geno(fake.f2, n.draws=8, step=2, err=0.001)
    qtl <- makeqtl(fake.f2, qc, qp, what="draws")
    summary(qtl)

[Package qtl version 1.46-2 Index]