processAssay-methods: Process assay tab data

In isatabr: Implementation for the ISA Abstract Model

Process assay tab data

Description

Process data from assay tab files

Process data from assay tab files with technology type mass spectrometry (ms). Processing those files requires the xcms package to be installed.

Process data from assay tab files with technology type DNA microarray (ms). Processing those files requires the Biobase and affy packages to be installed.

Usage

processAssay(isaObject, aTabObject, type = c("raw", "derived"))

## S4 method for signature 'ISA,assayTab,character'
processAssay(isaObject, aTabObject, type = c("raw", "derived"))

## S4 method for signature 'ISA,msAssayTab,character'
processAssay(isaObject, aTabObject, type = c("raw", "derived"))

## S4 method for signature 'ISA,microarrayAssayTab,character'
processAssay(isaObject, aTabObject, type = c("raw", "derived"))

Arguments

isaObject	An object of the ISA.
aTabObject	An object of the microarrayAssayTab.
type	A character string indicating which data files should be processed, either "raw" for raw data files, or "derived" for derived data files. The file names are taken from the corresponding column in the aTabObject.

Examples

### Atwell data.

## Read example Atwell data set.
isaObject1 <- readISATab(path = file.path(system.file("extdata/Atwell",
                                          package = "isatabr")))

## Get assay tabs for isaObject1.
aTabObjects <- getAssayTabs(isaObject1)

## Process assay data.
isaDat <- processAssay(isaObject = isaObject1,
                      aTabObject = aTabObjects$s_study1.txt$a_study1.txt,
                       type = "derived")

## Display first rows and columns.
head(isaDat[, 1:10])


### faahKO data. - This requires the xcms package to be installed.
## Read ISA-Tab files for faahKO.
if (requireNamespace("xcms")) {
  isaObject3 <- readISATab(path = file.path(system.file("extdata/faahKO",
                                            package = "isatabr")))

  ## Get assay tabs for isaObject3.
  aTabObjects3 <- getAssayTabs(isaObject3)

  ## Process assay data.
  isaDat3 <-
    processAssay(isaObject = isaObject3,
                 aTabObject = aTabObjects3$s_Proteomic_profiling_of_yeast.txt$a_metabolite.txt,
                 type = "raw")

  ## Display output.
  isaDat3
  }

isatabr documentation built on Aug. 19, 2022, 5:17 p.m.