easyRNASeq (version 2.8.2)

easyRNASeq summarization methods: Count methods for RNAseq object

Description

Summarize the read counts per exon, feature, gene, transcript or island.

• exonCounts: for that summarization, reads are summarized per exons. An "exon" field is necessary in the annotation object for this to work. SeeeasyRNASeq annotation methodsfor more details on the annotation object.

featureCounts is similar to the 'exons' one. This is just a wrapper to summarize count for genomic features that are not exon related. I.e. one could use it to measure eRNAs. Again, a "feature" field is necessary in the annotation object for this to work. geneCounts sums the counts per either bestExons or geneModels. In either case, the annotation object needs to contain both an "exon" and a "gene" field. islandCounts sums the counts per computed islands. transcriptCounts sums the counts obtained by exons into their respective transcripts. Note that this often result in counting some reads several times. For this function to work you need both an "exon" and a "transcript" field in your annotation object. To avoid this, one could create transcript specific synthetic exons, i.e. features that would be unique to a transcript. To offer this possibility, transcripts count can be summarized from "features", in which case the annotation object need to have both the "feature" and "transcript" fields defined.

Usage

exonCounts(obj)
featureCounts(obj)
transcriptCounts(obj,from="exons")
geneCounts(obj,summarization=c("bestExons","geneModels"),...)
islandCounts(obj,force=FALSE,...)

Arguments

obj

An object derived from class RNAseq,can be a matrix for RPKM, see details

force

For islandCount, force RNAseq to redo findIsland

from

either "exons" or "features" can be used to summarize per transcript

summarization

Method use for summarize genes

...

See details

Value

• A numeric vector containing count per exon, feature, gene or transcript.

itemize

• geneCounts: additional options for the.geneModelSummarization

item

islandCounts: additional options for findIslands

Details

...

See Also

easyRNASeq annotation methods .geneModelSummarization findIslands

Examples

## create an RNAseq object
	## summarizing 4 bam files by exons
	rnaSeq <- easyRNASeq(system.file(
                                 "extdata",
                                 package="RnaSeqTutorial"),
                     organism="Dmelanogaster",
                     chr.sizes=as.list(seqlengths(Dmelanogaster)),
                     readLength=36L,
                     annotationMethod="rda",
                     annotationFile=system.file(
                       "data",
                       "gAnnot.rda",
                       package="RnaSeqTutorial"),
                     format="bam",
                     count="exons",
                     pattern="[A,C,T,G]{6}\\.bam$",
                     outputFormat="RNAseq")
	## summing up the exons by transcript
	rnaSeq <- transcriptCounts(rnaSeq)