easyRNASeq-summarization-methods: Count methods for RNAseq object
In easyRNASeq: Count summarization and normalization for RNA-Seq data

Description Usage Arguments Details Value Author(s) See Also Examples

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. See easyRNASeq annotation methods for 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.

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

`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

... for

geneCounts: additional options for the .geneModelSummarization
islandCounts: additional options for findIslands

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

Nicolas Delhomme

easyRNASeq annotation methods .geneModelSummarization findIslands

## Not run: 
library(BSgenome.Dmelanogaster.UCSC.dm3)

 # get the example data files
 tdir <- tutorialData()

 # get an example annotation file - we retrieve it from GitHub using curl
 gAnnot.rda <- fetchData("gAnnot.rda")

	# create an RNAseq object
	# summarizing 2 bam files by exons
	rnaSeq <- easyRNASeq(tdir,
                     organism="Dmelanogaster",
                     chr.sizes=seqlengths(Dmelanogaster),
                     readLength=36L,
                     annotationMethod="rda",
                     annotationFile=gAnnot.rda,
                     format="bam",
                     count="exons",
                     pattern="[A,C,T,G]{6}\\.bam$",
                     outputFormat="RNAseq")
	# summing up the exons by transcript
	rnaSeq <- transcriptCounts(rnaSeq)

## End(Not run)