pairwiselogFC: Compute pairwise log-fold changes
In MKomics: Omics Data Analysis

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

The function computes pairwise log-fold changes.

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

`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.
`...`	optional arguments to `ave`.

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

The implementation is in certain aspects analogously to pairwise.t.test.

Vector with pairwise log-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.logfc(x, g)

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