pairwise.fc {MKmisc}R Documentation

Compute pairwise fold changes

Description

This function computes pairwise fold changes. It also works for logarithmic data.

Usage

pairwise.fc(x, g, ave = mean, log = TRUE, base = 2, mod.fc = TRUE, ...)

Arguments

x numeric vector.
g grouping vector or factor
ave function to compute the group averages.
log logical. Is the data logarithmic?
base If log = TRUE, the base which was used to compute the logarithms.
mod.fc logical. Return modified fold changes? (see details)
... optional arguments to ave.

Details

The function computes pairwise fold-changes between groups, where the group values are aggregated using the function which is given by the argument ave.

The fold-changes are returned in a slightly modified form if mod.fc = TRUE. Fold changes FC which are smaller than 1 are reported as to -1/FC.

The implementation is comparable to pairwise.t.test.

Value

Vector with pairwise fold-changes.

Author(s)

Matthias Kohl Matthias.Kohl@stamats.de

See Also

pairwise.t.test

Examples

set.seed(13)
x <- rnorm(100) ## assumed as log2-data
g <- factor(sample(1:4, 100, replace = TRUE))
levels(g) <- c("a", "b", "c", "d")
pairwise.fc(x, g)

## some small checks
res <- by(x, list(g), mean)
2^(res[[1]] - res[[2]]) # a vs. b
-1/2^(res[[1]] - res[[3]]) # a vs. c
2^(res[[1]] - res[[4]]) # a vs. d
-1/2^(res[[2]] - res[[3]]) # a vs. d
-1/2^(res[[2]] - res[[4]]) # b vs. d
2^(res[[3]] - res[[4]]) # c vs. d

[Package MKmisc version 0.3 Index]