readExpSet: Reads align number or gptm or rpmg value from all given...

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

Opens multiple BAM-files and reads aligns for selected gene for each file. Number of alignes is counted.

Usage

readExpSet(bam, idx, val="nAligns", phenoData, expData)

Arguments

bam	Vector of BAM-files

idx	Vector of index files (optional)

val	"gptm", "rpmg" or "nAligns". Value type which is written to ExpressionSet matrix (nAligns = read count).

phenoData

AnnotatedDataFrame. Each BAM-file must correspond to one identifier.

expData

MIAME. Optional. Experiment data which can be added to ExpressionSet

Value

ExpressionSet

Author(s)

Wolfgang Kaisers

Examples

# A) Names of BAM-files
bam <- character(2)
bam[1] <- system.file("extdata", "rna_fem.bam", package="spliceSites")
bam[2] <- system.file("extdata", "rna_mal.bam", package="spliceSites")

# B) Experiment Profile
prof <- data.frame(gender=c("f", "m"))
meta <- data.frame(labelDescription=names(prof), row.names=names(prof))
pd <- new("AnnotatedDataFrame", data=prof, varMetadata=meta)

# C) Read ExpressionSet
es <- readExpSet(bam, phenoData=pd)

# D) Annotate ExpressionSet
ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites")
juc <- loadGenome(ucf)
ann <- annotate(es, juc)
phenoData(es) <- ann

spliceSites documentation built on May 6, 2019, 3:05 a.m.