getCounts-methods: Extract read counts
In Senbee/Sequgio: Isoform expression estimation based on RNA-seq data

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

Retrive the number of read counts in each exon or junction.

1 2	## S4 method for signature 'seqCounts' getCounts(Object)

Object

an object of class seqCounts.

A list contains the number of reads in exons and junctions.

Stefano Calza <stefano.calza@unibs.it>, Chen Suo, Agus Salim and Yudi Pawitan

Suo C, Calza S, Salim A, Pawitan Y. Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. Bioinformatics. 2014 Feb 15;30(4):506-13

makeXmatrix, fitModels

## Not run: 
library(RNAseqData.HNRNPC.bam.chr14)
data("TxDb")

bflist <- BamFileList(RNAseqData.HNRNPC.bam.chr14_BAMFILES,asMates=TRUE)

seqObj <- setCounts(bflist,txdb,fileName='test')

param <- SerialParam()

doCounts(seqObj,mcpar=param)
bigM <- getCounts(seqObj)
allCounts <- as.matrix(bigM)

## End(Not run)