GSCollectionIndex {EGSEA} | R Documentation

## The GSCollectionIndex class

### Description

The `GSCollectionIndex` class stores an indexed gene set collection.

The operator `$` extracts a slot from an object of class GSCollectionIndex.

`summary` displays a brief summary of a gene set collection

`show` displays the details of a gene set collection

`getSetByName` retrieves the details of a given gene set indicated by name

`getSetByID` retrieves the details of a given gene set indicated by ID

### Usage

    ## S4 method for signature 'GSCollectionIndex'
    x$name

    ## S4 method for signature 'GSCollectionIndex'
    summary(object)

    ## S4 method for signature 'GSCollectionIndex'
    show(object)

    getSetByName(object, set.name)

    getSetByID(object, id)

### Arguments

`x` | GSCollectionIndex, the indexed gene set collection generated from `buildIdx`, `buildMSigDBIdx`, `buildKEGGIdx`, `buildGeneSetDBIdx`, and `buildCustomIdx`.
`name` | character, the slot name
`object` | GSCollectionIndex, the indexed gene set collection generated from `buildIdx`, `buildMSigDBIdx`, `buildKEGGIdx`, `buildGeneSetDBIdx`, and `buildCustomIdx`.
`set.name` | character, a vector of gene set names as they appear in `topSets`.
`id` | character, a vector of gene set IDs as they appears in the `plotSummary`.

### Details

The `GSCollectionIndex` is used by `buildIdx`, `buildCustomIdx`, `buildKEGGIdx`, `buildMSigDBIdx` and `buildGeneSetDBIdx`.

### Value

`$` returns the selected slot data.

`summary` does not return data.

`show` does not return data.

`getSetByName` returns a list of annotation records

`getSetByID` returns a list of the annotation records.

### Slots

`original`

  list, the original gene sets

`idx`

  list, the gene set indexes

`anno`

  data.frame, the annotations of the gene sets

`featureIDs`

  character, vector of the original Entrez IDs that are used in the indexing procedure

`species`

  character, the species name

`name`

  character, the name of the gene set collection

`label`

  character, a label to distnguish this collection

`version`

  character, the database version from which the collection was extracted

`date`

  character, the update/download date of the database from other collections

### Examples

    # Example of GSCollectionIndex
    library(EGSEAdata)
    data(il13.data)
    v = il13.data$voom
    gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human",
    			msigdb.gsets="none",
             kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
    print(gs.annots[[1]]$name)

    # Example of summary
    library(EGSEAdata)
    data(il13.data)
    v = il13.data$voom
    gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human",
    			msigdb.gsets="none",
             kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
    summary(gs.annots[[1]])

    # Example of show
    library(EGSEAdata)
    data(il13.data)
    v = il13.data$voom
    gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human",
    			msigdb.gsets="none",
             kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
    show(gs.annots[[1]])

    # Example of getSetByName
    library(EGSEAdata)
    data(il13.data)
    v = il13.data$voom
    gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human",
    			msigdb.gsets="none",
             kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
    getSetByName(gs.annots[[1]], "Asthma")

    # Example of getSetByID
    library(EGSEAdata)
    data(il13.data)
    v = il13.data$voom
    gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human",
    			msigdb.gsets="none",
             kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
    getSetByID(gs.annots[[1]], "hsa04060")

[Package EGSEA version 1.12.0 Index]