getLabels {maigesPack} | R Documentation

## Method getLabels to pick gene and sample labels

### Description

Generic function `getLabels` to extract labels given an ID to genes or samples.

### Usage

    getLabels(obj, labelID=NULL, sLabel=TRUE)

    ## Default S3 method:
    getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

    ## S3 method for class 'maigesDE'
    getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

    ## S3 method for class 'maigesDEcluster'
    getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

    ## S3 method for class 'RGList'
    getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

    ## S3 method for class 'MAList'
    getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

    ## S3 method for class 'marrayRaw'
    getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

    ## S3 method for class 'marrayNorm'
    getLabels(obj=NULL, labelID=NULL, sLabel=TRUE)

### Arguments

`obj` | object to look for labels. Methods defined for classes `maigesRaw`, `maiges`, `maigesDE`, `maigesDEcluster`, `RGList`, `MAList`, `marrayRaw` and `marrayNorm`.
`labelID` | character string with label name to be searched.
`sLabel` | logical indicating search in the sample labels, defaults to TRUE. If FALSE search is done for gene labels.

### Details

The name of gene labels are done by the names of the slot `Glabels` in objects of classes `maigesRaw` or `maiges`, the slot `GeneInfo` in objects of classes `maigesDE` or `maigesDEcluster`, the slot `genes` in objects of classes `RGList` or `MAList` and the slot `maGnames@maInfo` in objects of classes `marrayRaw` or `marrayNorm`. Equivalently, the name of sample labels are done by the names of the slots `Slabels`, `SampleInfo`, `targets` and `maTargets@maInfo`.

### Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

### Examples

    ## Loading dataset
    data(gastro)

    ## Getting the 'Tissue' label for samples in maigesRaw class object
    getLabels(gastro.raw, "Tissue", sLabel=TRUE)

    ## Getting the 'Type' label for samples in maigesNorm class object
    getLabels(gastro.summ, "Type", sLabel=TRUE)

    ## Getting the 'GeneName' label for genes (spots) in maigesRaw class object
    getLabels(gastro.raw, "GeneName", sLabel=FALSE)

    ## Getting the 'Annot' label for samples in maigesNorm class object
    getLabels(gastro.summ, "Annot", sLabel=FALSE)

[Package maigesPack version 1.56.0 Index]