Apply a function over contrasts

Helper function to run many pairwise comparisons using a contrast matrix

Usage

ApplyContrasts(
  data,
  analysis,
  name.prefix,
  contrasts,
  mode.slot = NULL,
  genes = NULL,
  verbose = FALSE,
  FUN,
  ...
)

data: the grandR object
analysis: a plain name, only used for status messages
name.prefix: the prefix for the new analysis name; a dot and the column names of the contrast matrix are appended; can be NULL (then only the contrast matrix names are used)
contrasts: contrast matrix that defines all pairwise comparisons, generated using GetContrasts
mode.slot: which slot to take expression values from
genes: restrict analysis to these genes; NULL means all genes
verbose: print status messages?
FUN: a function taking 1. the data matrix, 2. a logical vector indicating condition A and 3. a logical vector indicating condition B
...: further parameters forward to FUN

a new grandR object with added analysis tables (that were returned by FUN)

To implement most pairwise analyses, you only have to define FUN; see the source code of LFC for an example!