extractTestingResults {wrProteo} | R Documentation |
Extract Results From Moderated t-tests
Description
This function allows convenient access to results produced using the functions moderTest2grp
or moderTestXgrp
.
The user can define the threshold which type of multiple testing correction should be used
(as long as the multiple testing correction method was actually performed as part of testing).
Usage
extractTestingResults(
stat,
compNo = 1,
statTy = "BH",
thrsh = 0.05,
FCthrs = 1.5,
annotCol = c("Accession", "EntryName", "GeneName"),
nSign = 6,
addTy = c("allMeans"),
filename = NULL,
fileTy = "csvUS",
silent = FALSE,
debug = FALSE,
callFrom = NULL
)
Arguments
stat |
('MArrayLM'-object or list) Designed for the output from |
compNo |
(integer) the comparison number/index to be used |
statTy |
(character) the multiple-testing correction type to be considered when looking for significant changes with threshold |
thrsh |
(numeric) the threshold to be applied on |
FCthrs |
(numeric) Fold-Change threshold given as Fold-change and NOT log2(FC), default at 1.5 (for filtering at M-value =0.585) |
annotCol |
(character) column-names from the annotation to be included |
nSign |
(integer) number of significant digits whe returning results |
addTy |
(character) additional groups to add (so far only "allMeans" available) in addition to the means used in the pairwise comparison |
filename |
(character) optional (path and) file-name for exporting results to csv-file |
fileTy |
(character) file-type to be used with argument |
silent |
(logical) suppress messages |
debug |
(logical) display additional messages for debugging |
callFrom |
(character) allow easier tracking of messages produced |
Value
This function returns a limma-type MA-object (which can be handeled just like a list)
See Also
testRobustToNAimputation
, moderTestXgrp
or moderTest2grp
Examples
grp <- 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=""), paste(grp,c(1:2,1:3,1:3),sep="")))
t8[3:6,1:2] <- t8[3:6,1:2] +3 # augment lines 3:6 (c-f)
t8[5:8,c(1:2,6:8)] <- t8[5:8,c(1:2,6:8)] -1.5 # lower lines
t8[6:7,3:5] <- t8[6:7,3:5] +2.2 # augment lines
## expect to find C/A in c,d,g, (h)
## expect to find C/D in c,d,e,f
## expect to find A/D in f,g,(h)
library(wrMisc) # for testing we'll use this package
test8 <- moderTestXgrp(t8, grp)
extractTestingResults(test8)