pairwiselogFC: Compute pairwise log-fold changes

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

Description

The function computes pairwise log-fold changes.

Usage

1
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 Matthias.Kohl@stamats.de

See Also

pairwise.t.test

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
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 Aug. 8, 2021, 5:06 p.m.