writeISAtab {isatabr}

Write ISA-Tab object.

Description

Write ISA-Tab object to files. The investigation file, study files and assay files are written to the folder specified in path.

It is also possible to write only the investigation file, one or more study files, or one or more assay files using the respective functions.

Usage

writeISAtab(isaObject, path = getwd())

writeInvestigationFile(isaObject, path = getwd())

writeStudyFiles(
  isaObject,
  studyFilenames = getStudyFileNames(isaObject),
  path = getwd()
)

writeAssayFiles(
  isaObject,
  assayFilenames = unlist(getAssayFileNames(isaObject)),
  path = getwd()
)

Arguments

isaObject

An object of the ISA-class.

path

A character vector with the name of the directory to which the file(s) should be written. The default value is the current working directory.

studyFilenames

A character vector indicating the study files that should be written. Default all study files in isaObject are written.

assayFilenames

A character vector indicating the assay files that should be written. Default all assay files in isaObject are written.

Value

No return value, files are written to path.

Examples

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

## Write content of ISA object to a temporary directory.
writeISAtab(isaObject = isaObject1,
           path = tempdir())

## Write investigation file to a temporary directory.
writeInvestigationFile(isaObject = isaObject1,
                       path = tempdir())

## Write study file to a temporary directory.
writeStudyFiles(isaObject = isaObject1,
                studyFilenames = "s_study1.txt",
                path = tempdir())

## Write assay file to a temporary directory.
writeAssayFiles(isaObject = isaObject1,
                assayFilenames = "a_study1.txt",
                path = tempdir())