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

In wrProteo: Proteomics Data Analysis Functions

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
)

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

Value

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

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"))

wrProteo documentation built on April 12, 2025, 1:16 a.m.