easyRNASeq (version 2.8.2)

easyRNASeq accessors: Accessors for RNAseq class

Description

These functions and generics define `accessors` (to get and set values) for objects in the easyRNASeq package.

Usage

genomicAnnotation(obj)
readCounts(obj,count=c("exons","features","genes","islands","transcripts"),
summarization=c("bestExons","geneModels"),unique=FALSE)
genomicAnnotation(obj) <- value

Arguments

obj

An object derived from class RNAseq.

count

The type of count you want to access, 'genes','features','exons','transcripts' or 'islands'

summarization

If count is set to genes, precise the type of summarization, 'bestExons' or 'geneModels'

unique

For the 'exons' count only. Should the counts returned be unique for their identifier (i.e. the matrix row names)?

value

The replacement value.

Value

• Usually, the value of the corresponding slot, or other simple content described on the help page of easyRNASeq.

Examples

rnaSeq<-new("RNAseq")
##set organisme name of an RNAseq object
organismName(rnaSeq) <- "Dmelanogaster"
##get organisme name of an RNAseq object
orgName<-organismName(rnaSeq)