qtl (version 1.66)

subset.scanone: 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 scanone
subset(x, chr, lodcolumn, ...)

Value

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

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.

Author

Karl W Broman,

See Also

summary.scanone, scanone

Examples

data(fake.bc)
fake.bc <- subset(fake.bc, chr=16:19)
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")