corColumnOrder: Order Columns In List Of Matrixes, Data.frames And Vectors
View source: R/corColumnOrder.R
| corColumnOrder | R Documentation |
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 |
sampNames |
(character) column-names in desired order for output (its content must match colnames of |
replNames |
(character) option for replacing column-names by new/different colnames; should be vector of NEW column-names (in order as input from |
useListElem |
(character) in case |
annotElem |
(character) name of list-element of |
newNames |
depreciated, pleqse use |
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"))
