transforming: Transformation of the dataMatrix

In SciDoPhenIA/phenomis: Analysis of single and multiple phenomic data sets

Transformation of the dataMatrix

Description

Transformation of the dataMatrix intensities

Usage

transforming(
  x,
  method.vc = c("log2", "log10", "sqrt")[1],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'MultiAssayExperiment'
transforming(
  x,
  method.vc = c("log2", "log10", "sqrt")[1],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'SummarizedExperiment'
transforming(
  x,
  method.vc = c("log2", "log10", "sqrt")[1],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'MultiDataSet'
transforming(
  x,
  method.vc = c("log2", "log10", "sqrt")[1],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'ExpressionSet'
transforming(
  x,
  method.vc = c("log2", "log10", "sqrt")[1],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

Arguments

x	An S4 object of class SummarizedExperiment or MultiAssayExperiment (ExpressionSet and MultiDataSet are deprecated)
method.vc	character(): type of transformation (either 'log2', 'log10', or 'sqrt'); in case of a MultiAssayExperiment, distinct methods may be provided for each dataset
report.c	Character: File name with '.txt' extension for the printed results (call to sink()'); if 'interactive' (default), messages will be printed on the screen; if 'none', no verbose will be generated

Value

SummarizedExperiment (or MultiAssayExperiment) including the (list of) matrix with transformed intensities

Examples

sacurine.se <- reading(system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis"))
sacurine.se <- correcting(sacurine.se)
sacurine.se <- sacurine.se[, colData(sacurine.se)[, "sampleType"] != "pool"]
sacurine.se <- transforming(sacurine.se)
# MultiDataSet
prometis.mae <- reading(system.file("extdata/prometis", package = "phenomis"))
prometis.mset <- transforming(prometis.mset)

SciDoPhenIA/phenomis documentation built on June 9, 2022, 11:54 p.m.