R: Subsetting two-dimensional permutation test results

subset.scantwoperm {qtl} | R Documentation

## Subsetting two-dimensional permutation test results

### Description

Pull out results for a specified set LOD columns from permutation results from `scantwo`.

### Usage

    ## S3 method for class 'scantwoperm'
    subset(x, repl, lodcolumn, ...)
    ## S3 method for class 'scantwoperm'
    x[repl, lodcolumn]

### Arguments

`x` | Permutation results from `scantwo`, run with `n.perm`>0.
`repl` | A vector specifying which permutation replicates to keep or (if negative) omit. Ignored in case of X-chr specific permutations
`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` permutation results, but with only the specified subset of the data.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`summary.scantwoperm`, `scantwo`, `c.scantwoperm`, `rbind.scantwoperm`

### Examples

    data(fake.bc)

    fake.bc <- calc.genoprob(fake.bc, step=0)
    operm <- scantwo(fake.bc, method="hk", pheno.col=1:2, n.perm=5)
    operm2 <- subset(operm, lodcolumn=2)

    # alternatively
    operm2alt <- operm[,2]

[Package qtl version 1.46-2 Index]