cleanListCoNames {wrProteo}

Selective batch cleaning of sample- (ie column-) names in list

Description

This function allows to manipulate sample-names (ie colnames of abundance data) in a batch-wise manner from data stored as multiple matrixes or data.frames of a list. Import functions such as readMaxQuantFile() organize initial flat files into lists (of matrixes) of the different types of data. Many times all column names in such lists carry long names including redundant information, like the overall experiment name or date, etc. The aim of this function is to facilitate 'cleaning' the sample- (ie column-) names to obtain short and concise names. Character terms to be removed (via argument rem) and/or replaced/subsitituted (via argument subst) should be given as they are, characters with special behaviour in grep (like '.') will be protected internally. Note, that the character substitution part will be done first, and the removal part (without character replacement) afterwards.

Usage

cleanListCoNames(
  dat,
  rem = NULL,
  subst = c("-", "_"),
  lstE = c("raw", "quant", "counts"),
  mathOper = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

dat

(list) main input

rem

(character) character string to be removed, may be named 'left' and 'right' for more specific exact pattern matching (this part will be perfomed before character substitutions by subst)

subst

(character of length=2, or matrix with 2 columns) pair(s) of character-strings for replacement (1st as search-item and 2nd as replacement); this part is performed after character-removal via rem

lstE

(character, length=1) names of list-elements where colnames should be cleaned

mathOper

(character, length=1) optional mathematical operation on numerical part of sample-names (eg mathOper='/2' for deviding numeric part of colnames by 2)

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

callFrom

(character) allow easier tracking of messages produced

Value

This function returns a list (equivalent to input dat)

See Also

grep

Examples

dat1 <- matrix(1:12, ncol=4, dimnames=list(1:3, paste0("sample_R.",1:4)))
dat1 <- list(raw=dat1, quant=dat1, notes="other..")
cleanListCoNames(dat1, rem=c(left="sample_"), c(".","-"))