wrProteo (version 1.5.0)

corColumnOrder: Order columns in list of matrixes (or matrix)

Description

This function orders columns in list of matrixes (or matrix) according to argument sampNames. This function can be used to adjut/correct the order of samples after reading data using readMaxQuantFile(), readPDExport() etc. The input may also be MArrayLM-type object from package limma or from moderTestXgrp or moderTest2grp.

Usage

corColumnOrder(
  dat,
  sampNames,
  useListElem = c("quant", "raw"),
  silent = FALSE,
  callFrom = NULL
)

Arguments

dat

(matrix, list or MArrayLM-object from limma) main input of which columns should get re-ordered, may be output from moderTestXgrp or moderTest2grp.

sampNames

(character) column-names in desired order for output

useListElem

(character) in case dat is list, all list-elements who's columns should get (re-)ordered

silent

(logical) suppress messages

callFrom

(character) allow easier tracking of message(s) produced

Value

object of same class as input dat

See Also

moderTestXgrp for single comparisons, order

Examples

# NOT RUN {
grp <- factor(rep(LETTERS[c(3,1,4)], c(2,3,3)))
dat1 <- matrix(1:15, ncol=5, dimnames=list(NULL,c("D","A","C","E","B")))
corColumnOrder(dat1,sampNames=LETTERS[1:5])  

dat1 <- list(quant=dat1,raw=dat1)
  dat1
corColumnOrder(dat1,sampNames=LETTERS[1:5]) 
# }