pairwiseFC: Compute pairwise fold changes
In MKomics: Omics Data Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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`.

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 in certain aspects analogously to pairwise.t.test.

Vector with pairwise fold changes.

Matthias Kohl Matthias.Kohl@stamats.de

pairwise.t.test

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]]) # b vs. c
-1/2^(res[[2]] - res[[4]]) # b vs. d
2^(res[[3]] - res[[4]]) # c vs. d