calcDif: Create a "difference" gene expression set

In january3/myfuncs: loads a few functions I often need

Description

This function takes a limma EList object and calculates the pairwise differences between two groups of samples.

Usage

calcDif(E, pairID, groupID)

Arguments

E	A limma EList object.
pairID	A factor used to match the samples. Incomplete pairs are allowed, but they will be ignored.
groupID	A factor categorizing the samples in one of two groups. This factor must have exactly two levels.

Details

First, the function construct a list of pair IDs which are present in both groups. Next, for each sample in the first group, the corresponding sample from the second group is subtracted from it. This is of course done for every variable (gene or otherwise) in E.

Value

EList object with as many samples as there are pairs present in both groups. In the target slot of the object, a new column called difID is created (if absent) or modified, and includes information about the subtraction.

january3/myfuncs documentation built on April 1, 2020, 4:42 a.m.