wrMisc: makeMAList – R documentation

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makeMAList

make MA-List object

Description

makeMAList extracts sets of data-pairs (like R & G series) and makes MA objects as MA-List object (eg for ratio oriented analysis). The grouping of columns as sets of replicate-measurements is done according to argumnet 'MAfac'. The output is fully compatible to functions of package limma (Bioconductor).

Usage

makeMAList(
  mat,
  MAfac,
  useF = c("R", "G"),
  isLog = TRUE,
  silent = FALSE,
  callFrom = NULL
)

Arguments

`mat`	main input matrix
`MAfac`	(factor) factor orgnaizing columns of 'mat' (if `useF` contains the default 'R' and 'G', they should also be part of `MAfac`)
`useF`	(character) two specific factor-leves of `MAfac` that will be used/extracted
`isLog`	(logical) tell if data is already log2 (will be considered when computing M and A values)
`silent`	(logical) suppress messages
`callFrom`	(character) allows easier tracking of message(s) produced

Value

limma-type "MAList" containing M and A values

Examples

set.seed(2017); t4 <- matrix(round(runif(40,1,9),2),ncol=4,
  dimnames=list(letters[c(1:5,3:4,6:4)],c("AA1","BB1","AA2","BB2")))
makeMAList(t4,gl(2,2,labels=c("R","G")))

wrMisc

Analyze Experimental High-Throughput (Omics) Data

v1.5.4

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release