pairwiselogFC: Compute pairwise log-fold changes

In MKmisc: Miscellaneous Functions from M. Kohl

Compute pairwise log-fold changes

Description

The function computes pairwise log-fold changes.

Usage

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

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.
...	optional arguments to ave.

Details

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.

Value

Vector with pairwise log-fold changes.

Author(s)

Matthias Kohl [e-mail]

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.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

MKmisc documentation built on Nov. 20, 2022, 1:05 a.m.