readExpSet {spliceSites} | R Documentation

## Reads align number or gptm or rpmg value from all given BAM-files and all identified align gaps into ExpressionSet.

### 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

[Package spliceSites version 1.31.0 Index]