combineRedundLinesInList {wrMisc}

Combine Redundant Lines In List

Description

This function provides help for combining/summarizing lines of numeric data which may be summaried according to reference vector or matrix of annotation (part of the same input-list). The data and reference will be aligned and data corresponding to redundant information be combined/summarized.

Usage

combineRedundLinesInList(
  lst,
  refNa = "ref",
  datNa = "quant",
  refColNa = "GeneName",
  supRefColNa = NULL,
  summarizeType = "av",
  NA.rm = TRUE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

lst

(list) main input, containing matrix or data.frame of numeric data (see datNa and annotation (see refNa) and possibly unrelated stuff

refNa

(character) name of list-element containing annotation

datNa

(character) name(s) of list-element(s) containing numeric/quantitation data

refColNa

(character) in case the list-element to be used as reference is matrix or data.frame, the column to be used must be specified here

supRefColNa

(character) in case the lst$refNa has no rownames, the content of column lst$supRefColNa will be used instead

summarizeType

(character) the summarization method gets specified here; so far 'sum','av','med','first' and 'last' are implemented

NA.rm

(logical) pass to summarizing functions order to omit NAs, defaults to TRUE

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

callFrom

(character) allow easier tracking of messages produced

Details

All input data should be in a list, ie one or multipl matrix or data.frame for numeric data (see argument datNa), as well as the reference (see argument refNa). The refgerence may be a named character vecor or a matrix for which the column to be used should be specified using the argument refColNa. In case the annotation is a matrix, the rownames will be used as unique/independent identifyers to adjust potentially different order of numeric data and annotation. In absence of rownames, an additional column supRefColNa of the annotation may be designed for adjusting the order of annotation and numeric data.

The numeric list may contain multiple matrixes or data.frames which will all be summarized by the same procedure as long as they have the same initial dimensions and are specified by refNa.

Please note that all other list elements from input not specified by refNa (or datNa) will be maintained in the output just as they are.

Value

This function returns a list of same length as input

See Also

findRepeated, firstOfRepLines, organizeAsListOfRepl, combineRedBasedOnCol

Examples

x1 <- list(quant=matrix(11:34, ncol=3, dimnames=list(letters[8:1], LETTERS[11:13])), 
  annot=matrix(paste0(LETTERS[c(1:4,6,3:5)],LETTERS[c(1:4,6,3:5)]), ncol=1, 
  dimnames=list(paste(letters[1:8]),"xx")) )
combineRedundLinesInList(lst=x1, refNa="annot", datNa="quant", refColNa="xx")