wrMisc: makeNRedMatr – R documentation

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makeNRedMatr

Make non-redundant matrix

Description

makeNRedMatr takes matrix or data.frame 'dat' to summarize redundant lines (column argument iniID) along method specified in summarizeRedAs to treat all lines with redundant iniID by same approach (ie for all columns the line where specified column is at eg max = 'maxOfRef' ). If no name given, the function will take the last numeric (factors may be used - they will be read as levels).

Usage

makeNRedMatr(
  dat,
  summarizeRedAs,
  iniID = "iniID",
  retDataFrame = TRUE,
  callFrom = NULL,
  silent = FALSE,
  debug = FALSE
)

Arguments

`dat`	(matrix or data.frame) main input for making non-redundant
`summarizeRedAs`	(character) summarization method(s), typical choices 'median','mean','min' or 'maxOfRef','maxAbsOfRef' for summarizing according to 1 specified column, may be single method for all or different method for each column (besides col 'iniID') or special method looking at column (if found, first of special methods used, everything else not considered).
`iniID`	(character) column-name used as initial ID (default="iniID")
`retDataFrame`	(logical) if TRUE, check if text-columns may be converted to data.frame with numeric
`callFrom`	(character) allows easier tracking of message(s) produced
`silent`	(logical) suppress messages
`debug`	(logical) for bug-tracking: more/enhanced messages

Value

(numeric) matrix or data.frame with summarized data and add'l col with number of initial redundant lines

Examples

t3 <- data.frame(ref=rep(11:15,3),tx=letters[1:15],
  matrix(round(runif(30,-3,2),1),nc=2),stringsAsFactors=FALSE)
by(t3,t3[,1],function(x) x)
t(sapply(by(t3,t3[,1],function(x) x), summarizeCols, me="maxAbsOfRef"))
(xt3 <- makeNRedMatr(t3, summ="mean", iniID="ref"))
(xt3 <- makeNRedMatr(t3, summ=unlist(list(X1="maxAbsOfRef")), iniID="ref"))

wrMisc

Analyze Experimental High-Throughput (Omics) Data

v1.5.4

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release