ISATab-class {Risa} | R Documentation

## Class `"ISATab"`, a class for maintaing ISATab information

### Description

This class maintains information from an ISATab dataset, including an investigation file, one or more study files, and one or more assay files for each study file.

### Objects from the Class

Objects can be created by calls of the form `new("ISATab", ...)`.

### Slots

`path`:

  Object of class `"character"`, it represents the path of the ISA-Tab dataset

`investigation.filename`:

  Object of class `"character"`, it represents the name of the Investigation file

`investigation.file`:

  Object of class `"data.frame"`, it is a data frame with the contents of the Investigation file

`investigation.identifier`:

  Object of class `"character"`, it is a string with the identifier for the investigation

`study.identifiers`:

  Object of class `"character"`, it is the list of study identifiers

`study.titles`:

  Object of class `"character"`, it is the list of study titles

`study.descriptions`:

  Object of class `"character"`, it is the list of study descriptions

`study.contacts`:

  Object of class `"character"`, it is the list of study contacts

`study.contacts.affiliations`:

  Object of class `"character"`, it is the list of affiliations of the study contacts

`study.filenames`:

  Object of class `"character"`, the names of the study files

`study.files`:

  Object of class `"list"`, a list of data frames wiht the contents of the study files

`assay.filenames`:

  Object of class `"character"`, the names of the assay files

`assay.filenames.per.study`:

  Object of class `"list"`, the names of the assay files according to the study they belong to

`assay.files`:

  Object of class `"list"`, a list of data frames with the contents of the assay files

`assay.files.per.study`:

  Object of class `"list"`, a list of data frames with the contents of the assay files divided per study they belong to

`assay.names`:

  Object of class `"list"`, which is a list of data frames, containing, per each assay file, the column of the assay file corresponding to the "Assay Name"

`assay.technology.types`:

  Object of class `"character"`, a list with the technology types corresponding to each assay

`assay.measurement.types`:

  Object of class `"character"`, a list with the names of the data files

`data.filenames`:

  Object of class `"list"`, a list with the names of the samples

`samples`:

  Object of class `"character"`

`samples.per.study`:

  Object of class `"list"`,

`samples.per.assay.filename`:

  Object of class `"list"`,the samples classified according to the assay filename they belong to

`assay.filenames.per.sample`:

  Object of class `"list"`, where each element is a list of assay file names per each sample name

`sample.to.rawdatafile`:

  Object of class `"list"`, a list of data frames with samples associated with raw data files

`sample.to.assayname`:

  Object of class `"list"`, maintains the association between samples and assay names

`rawdatafile.to.sample`:

  Object of class `"list"`, mantains the association raw data file and samples

`assayname.to.sample`:

  Object of class `"list"`, mantains the associations between assay names and samples

`factors`:

  Object of class `"list"`, which contains R 'factor' objects for each of the studies (with factor names and factor levels).

`treatments`:

  Object of class `"list"` of data frames with the combination of factor values, per study file, or a factor object, if there is a single study

`groups`:

  Object of class `"list"`, with one element per study file, and each element is a list of the samples for the corresponding treatment

`assay.tabs`:

  Object of class `"list"`, where each element is an object of the class `AssayTab` or its specialisations (`MSAssayTab` or `MicroarrayAssayTab`), representing the information of each of the assay files in the investigation.

### Methods

[

  `signature(x = "ISATab")`: ...

getRawDataFilenames

  `signature(.Object="ISATab", full.path=TRUE)`: get the raw data filenames for all the assays in the ISATab dataset

### Note

No notes yet.

### Author(s)

Alejandra Gonzalez-Beltran, isatools@googlegroups.com

### References

Risa is a component of the ISA software infrastructure http://isa-tools.org/. The source code and latest version can be found in the GitHub repository https://github.com/ISA-tools/Risa. Please, submit all 'bugs' and feature requests through https://github.com/ISA-tools/Risa/issues.

### See Also

`ISATab-methods`

### Examples

    showClass("ISATab")

[Package Risa version 1.34.0 Index]