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MKmisc (version 1.9)

pairwise.logfc: Compute pairwise log-fold changes

Description

The function computes pairwise log-fold changes.

Usage

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

Value

Vector with pairwise log-fold changes.

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.

Author

Matthias Kohl Matthias.Kohl@stamats.de

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.

See Also

Examples

Run this code
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

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