R: Subsetting the results of a 2-d genome scan

subset.scantwo {qtl} | R Documentation

## Subsetting the results of a 2-d genome scan

### Description

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

### Usage

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

### Arguments

`x` | An object of class `scantwo`, output from `scantwo`.
`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 `scantwo` object, but with only the specified subset of the data.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`summary.scantwo`, `scantwo`

### Examples

    data(fake.bc)

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

    summary(subset(out, chr=18:19))

[Package qtl version 1.41-6 Index]