ISAtab-class: Class '"ISATab"', a class for maintaing ISATab information

In ISA-tools/Risa: Converting experimental metadata from ISA-tab into Bioconductor data structures

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, [e-mail]

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")

ISA-tools/Risa documentation built on May 8, 2019, 1:25 p.m.