ISA-class: S4 Class ISA, initialization, extract- and replace-methods

Description Usage Arguments Details Slots Author(s)

Description

An S4 class to store information from an ISA-Tab dataset, including an investigation file, one or more study files, and one or more assay files for each study file.

When creating a new object of class ISA via: object <- new(Class = "ISA", path), the function initialize(.Object, path) is called to initialize and create the actual object. The initiliaze-method is seldomly used as a function itself.

Usage

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## S4 method for signature 'ISA'
initialize(.Object, path)

## S4 method for signature 'ISA,character'
x[i]

## S4 replacement method for signature 'ISA,character'
x[i] <- value

Arguments

.Object

character, name of the object of class ISA to be initialized

path

length-one character vector containing the path to the ISA-Tab files of the dataset.

x

S4 object of class ISA.

i

character, name of a slot to extract or replace.

value

ANY, replacement value for the slotname specified by i.

Details

x[i] defines a method to extract the information in the slot of an S4 object of class ISA by using a character vector specifying the name of the slot. Via x[i] <- value the value(s) in a slot of an S4 class object of class ISA can be replaced by means of specifying the name of the slot as a character vector. Below in the slot descriptions the character vectors to access specific slots are given.

Slots

path

A length-one character vector containing the path to the ISA-Tab dataset. The character vector to extract or replace this slot is "path".

iFileName

A length-one character vector containing the investigation filename (by definition starting with i_ and ending at .txt). The character vector to extract or replace this slot is "Investigation File Name".

oSR

A data.frame containing the "ONTOLOGY SOURCE REFERENCE" section of the investigation file. The character vector to extract or replace this slot is "ONTOLOGY SOURCE REFERENCE".

invest

A data.frame containing the "INVESTIGATION" section of the investigation file. The character vector to extract or replace this slot is "INVESTIGATION".

iPubs

A data.frame containing the "INVESTIGATION PUBLICATIONS" section of the investigation file. The character vector to extract or replace this slot is "INVESTIGATION PUBLICATIONS".

iContacts

A data.frame containing the "INVESTIGATION CONTACTS" section of the investigation file. The character vector to extract or replace this slot is "INVESTIGATION CONTACTS".

study

A list of data.frames containing the "STUDY" sections of the investigation file. Each study has its own section and the study identifier is used to name each element in the list. The character vector to extract or replace this slot is "STUDY".

sDD

A list of data.frames containing the "STUDY DESIGN DESCRIPTORS" sections of the investigation file. Each study has its own section and the study identifier is used to name each element in the list. The character vector to extract or replace this slot is "STUDY DESIGN DESCRIPTORS".

sPubs

A list of data.frames containing the "STUDY PUBLICATIONS" sections of the investigation file. Each study has its own section and the study identifier is used to name each element in the list. The character vector to extract or replace this slot is "STUDY PUBLICATIONS".

sFacts

A list of data.frames containing the "STUDY FACTORS" sections of the investigation file. Each study has its own section and the study identifier is used to name each element in the list. The character vector to extract or replace this slot is "STUDY FACTORS".

sAssays

A list of data.frames containing the "STUDY ASSAYS" sections of the investigation file. Each study has its own section and the study identifier is used to name each element in the list. The character vector to extract or replace this slot is "STUDY ASSAYS".

sProts

A list of data.frames containing the "STUDY PROTOCOLS" sections of the investigation file. Each study has its own section and the study identifier is used to name each element in the list. The character vector to extract or replace this slot is "STUDY PROTOCOLS".

sContacts

A list of data.frames containing the "STUDY CONTACTS" sections of the investigation file. Each study has its own section and the study identifier is used to name each element in the list. The character vector to extract or replace this slot is "STUDY CONTACTS".

sFiles

A list of data.frames containing the "Study Files", containing the contents of the Study Table files belonging to the studies in the investigation. Each study has one Study Table file. The character vector to extract or replace this slot is "Study Files".

aFiles

A list of data.frames containing the "Assay Files", containing the contents of the Assay Table files belonging to the studies in the investigation. Each study can have multiple Assay Table files. Each element of the list is named by the Assay File Name. The character vector to extract or replace this slot is "Assay Files".

Author(s)

Maikel Verouden


mverouden/isatabr documentation built on April 21, 2019, 4:35 a.m.