R: Subsetting the results of a genome scan

subset.scanone {qtl} | R Documentation

## Subsetting the results of a genome scan

### Description

Pull out a specified set of chromosomes and/or LOD columns from `scanone` output.

### Usage

    ## S3 method for class 'scanone'
    subset(x, chr, lodcolumn, ...)

### Arguments

`x` | An object of class `scanone`, output from `scanone`.
`chr` | Optional vector specifying which chromosomes to keep. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
`lodcolumn` | A vector specifying which LOD columns to keep (or, if negative), omit. These should be between 1 and the number of LOD columns in the input `x`.
`...` | Ignored at this point.

### Value

The input `scanone` object, but with only the specified subset of the data.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`summary.scanone`, `scanone`

### Examples

    data(fake.bc)

    fake.bc <- calc.genoprob(fake.bc, step=2.5)
    out <- scanone(fake.bc, method="hk", pheno.col=1:2)

    summary(subset(out, chr=18:19), format="allpeaks")

[Package qtl version 1.46-2 Index]