wrProteo (version 1.13.1)

corColumnOrder: Order Columns In List Of Matrixes, Data.frames And Vectors

Description

This function orders columns in list of matrixes (or matrix) according to argument sampNames and also offers an option for changing names of columns. It was (initially) designed to adjust/correct the order of samples after import using readMaxQuantFile(), readProteomeDiscovererFile() etc. The input may also be MArrayLM-type object from package limma or from functions moderTestXgrp or moderTest2grp.

Usage

corColumnOrder(
  dat,
  sampNames,
  replNames = NULL,
  useListElem = c("quant", "raw", "counts"),
  annotElem = "sampleSetup",
  newNames = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function returns an object of same class as input dat (ie matrix, list or MArrayLM-object from limma)

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 (its content must match colnames of dat or replNames, if used)

replNames

(character) option for replacing column-names by new/different colnames; should be vector of NEW column-names (in order as input from dat !), allows renaming colnames before defining new order

useListElem

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

annotElem

(character) name of list-element of dat with annotation data to get in new order

newNames

depreciated, pleqse use replNames instead

silent

(logical) suppress messages

debug

(logical) display additional messages for debugging

callFrom

(character) allows easier tracking of messages produced

See Also

readMaxQuantFile, readProteomeDiscovererFile; moderTestXgrp or moderTest2grp

Examples

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])

dat2 <- list(quant=dat1, raw=dat1)
dat2
corColumnOrder(dat2, sampNames=LETTERS[1:5])
corColumnOrder(dat2, sampNames=LETTERS[1:5], replNames=c("Dd","Aa","Cc","Ee","Bb"))