qtl (version 1.38-4)

subset.scanoneperm: Subsetting permutation test results

Description

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

Usage

## S3 method for class 'scanoneperm':
subset(x, repl, lodcolumn, \dots)
## S3 method for class 'scanoneperm':
[(x, repl, lodcolumn)

Arguments

x

Permutation results from scanone, run with n.perm>0.

repl

A vector specifying which permutation replicates to keep or (if negative) omit.

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 permutation results, but with only the specified subset of the data.

See Also

summary.scanoneperm, scanone, c.scanoneperm, cbind.scanoneperm, rbind.scanoneperm

Examples

data(fake.bc)
fake.bc <- subset(fake.bc, chr=16:19)
fake.bc <- calc.genoprob(fake.bc, step=5)
operm <- scanone(fake.bc, method="hk", pheno.col=1:2, n.perm=25)
operm2 <- subset(operm, lodcolumn=2)

# alternatively
operm2alt <- operm[,2]