readCounts: Summarize read overlaps
In estepi/ASpli: Analysis of alternative splicing using RNA-Seq

Description Usage Arguments Value Author(s) See Also Examples

Summarize read overlaps against all feature levels

1	readCounts(features, bam, cores, l, maxISize, minAnchor)

`features`	An object of class ASpliFeatures. It is a list of GRanges at gene, bin and junction level
`bam`	List of bam files
`l`	Read length of sequenced library. It is used for compute E1I and IE2 read summarization
`maxISize`	maximum intron expected size. Junctions longer than this size will be dicarded
`cores`	Number of cores to use. Default 1
`minAnchor`	Percentage of read thath sould be aligned in exon-intron boundary

An object of class ASpliCounts. Each slot is a dataframe containing features metadata and read counts. Summarization is reported at gene, bin, junction and intron flanking regions (E1I, IE2)

Estefania Mancini, Marcelo Yanovsky, Ariel Chernomoretz

Accesors: countsg, countsb, countsj,countse1i, countsie2,rdsg,rdsb Export: writeCounts

library(RNAseqData.HNRNPC.bam.chr14)
chr14 <- system.file("extdata","chr14.sqlite", package="ASpli")
genome <- loadDb(chr14)
features <- binGenome(genome)
targets <- data.frame(bam=RNAseqData.HNRNPC.bam.chr14_BAMFILES,
                       condition=c(rep("CT",4),rep("KD",4)))
bam <- loadBAM(targets)
counts <- readCounts(features, bam, l=100L, maxISize=50000)#OK
writeCounts(counts,output.dir="only_counts")