setCounts-methods: Create a container for read counts, a bigmatrix instance.

In Senbee/Sequgio: Isoform expression estimation based on RNA-seq data

Description

Create a container for read counts, a bigmatrix instance.

Usage

setCounts(bfl,txdb,sample.names=NULL,fileName=NULL,rootpath=getwd())

Arguments

bfl	a BamFile or BamFileList object
txdb	a reshaped (reshapeTxDb) TranscriptDb object
sample.names	Optional. Character vector of sample names, i.e. counts matrix column names
fileName	Optional. File name for bigmatrix description file
rootpath	Optional. Path to where to store the description file

Value

An object of class seqCounts.

Author(s)

Stefano Calza <[e-mail]>, Chen Suo, Agus Salim and Yudi Pawitan

References

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

Examples

## 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)

Senbee/Sequgio documentation built on May 9, 2019, 1:21 p.m.