Subsetting two-dimensional permutation test results
Pull out results for a specified set LOD columns from
permutation results from scantwo.
## S3 method for class 'scantwoperm' subset(x, repl, lodcolumn, ...) ## S3 method for class 'scantwoperm' x[repl, lodcolumn]
x |
Permutation results from
|
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 |
... |
Ignored at this point. |
The input scantwo permutation results, but with only the specified
subset of the data.
Karl W Broman, broman@wisc.edu
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]
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