readCounts: Summarize read overlaps

Description Usage Arguments Value Author(s) See Also Examples

Description

Summarize read overlaps against all feature levels

Usage

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

Arguments

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

Value

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)

Author(s)

Estefania Mancini, Marcelo Yanovsky, Ariel Chernomoretz

See Also

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

Examples

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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")

estepi/ASpli documentation built on May 16, 2019, 8:53 a.m.