qtl (version 1.66)

subset.scantwoperm: 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 scantwoperm
subset(x, repl, lodcolumn, ...)
# S3 method for scantwoperm
[(x, repl, lodcolumn)

Value

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

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.

Author

Karl W Broman,

See Also

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

Examples

data(fake.bc)
fake.bc <- subset(fake.bc, chr=18:19)
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]