getLabels: Method getLabels to pick gene and sample labels

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

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 <[e-mail]>

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)

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.