getPairwiseSetup: Extract Pairwise Testing Setup

Description

This function allows extacting, checking and combinig elements defining labels for pairwise comparisons.

Usage

getPairwiseSetup(
  pwGrpNa,
  grpNa = NULL,
  sep = NULL,
  combPwSep = "combine1",
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function returns a list with $ind with matrix of indexes to (sorted) pwGrpNa for each pairwise comparison; $pwGrpNames with matrix of pwGrpNa for each pairwise comparison; $sep for the separator found ; $pwGrpNa which recapitulates (sorted) pwGrpNa as factor

Arguments

pwGrpNa: (character) the names of pairwise-testing (ie 'concatenated' pwGrpNa using the separator sep )
grpNa: (character) the names of the groups of replicates (ie conditions) used to test
sep: (NULL or character, length=1) if not NULL the character-vector (of length=1) given will be used to split grpNa using stringsplit()
combPwSep: (character) sequence of separators for building combined names; may be combPwSep='combine1' or 'combine2'; will be used in pwSeparatorList()
silent: (logical) suppress messages
debug: (logical) additional messages for debugging
callFrom: (character) allow easier tracking of messages produced

Details

This function was designed to support functions exploiting pairwise testing results like plotting functions for Volcano-Plots etc.

Initially the function will check if the object given as argument pwGrpNa is an MAarrayLM-objects object and/or was created using moderTestXgrp. If yes, the function will try to extract names of groups, pairwise combinations and separator used from $setup, if present. If no $setup found this function will check through several elements in MAarrayLM-objects to gather all elements needed.

2) The separator sep is given and exact matches at both sides will be searched. However, if the character(s) from sep do appear inside pwGrpNa no matches will be found.

If some pwGrpNa are not found in grpNa this will be marked as NA.

Finally, if no testing result is given as input, basic parameters group-names, pairwise names and the separator to be used can be combined into a list.

Examples

Run this code

grp3 <- factor(rep(LETTERS[c(3,1,4)],c(2,3,3)))
set.seed(2017); t8 <- matrix(round(rnorm(208*8,10,0.4),2), ncol=8,
  dimnames=list(paste(letters[],rep(1:8,each=26),sep=""), paste0(grp3, c(1:2,1:3,1:3))))
test1 <- moderTestXgrp(t8, grp3)  
getPairwiseSetup(test1)