simpleRNASeq,BamFileList,RnaSeqParam-method {easyRNASeq} | R Documentation

## simpleRNASeq method

### Description

This function is a wrapper around the more low level functionalities of the package. It is the simplest way to get a `RangedSummarizedExperiment` object from a set of bam files. `RangedSummarizedExperiment` are containers meant to hold any Next-Generation Sequencing experiment results and metadata. The simpleRNASeq method replaces the `easyRNASeq` function to simplify the usability. It does the following:

- use `GenomicAlignments` for reading/pre-processing the BAM files.

- get the `annotations` depending on the selected parameters

- calculate the coverage from the provided file(s)

- `summarizes` the read counts according to the selected summarization

- returns a `RangedSummarizedExperiment` object.

### Usage

    ## S4 method for signature 'BamFileList,RnaSeqParam'
    simpleRNASeq(
      bamFiles = BamFileList(),
      param = RnaSeqParam(),
      nnodes = 1,
      verbose = TRUE,
      override = FALSE
    )

### Arguments

`bamFiles` | a `BamFileList` object
`param` | RnaSeqParam a `RnaSeqParam` object that describes the RNA-Seq experimental setup.
`nnodes` | The number of CPU cores to use in parallel
`verbose` | a logical to be report progress or not.
`override` | Should the provided parameters override the detected ones

### Value

returns a `RangedSummarizedExperiment` object.

### Author(s)

Nicolas Delhomme

### See Also

- For the input:

  - `AnnotParam`

  - `BamParam`

  - `RnaSeqParam`

- For the output: `RangedSummarizedExperiment`

- For related functions:

  - `BamFile`

  - `BamFileList` `getBamFileList`

### Examples

    # the data
    tdir <- tutorialData()
    annot <- fetchData("Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz")

     # create the BamFileList, get the BAM and BAI index files from the Bioc cache
     filenames <- dir(tdir,pattern="[A,T].*\\.bam$",full.names=TRUE)
     indexnames <- sapply(paste0(sub(".*_","",basename(filenames)),".bai"),fetchData)
     bamFiles <- getBamFileList(filenames,indexnames)

      # create the AnnotParam
      annotParam <- AnnotParam(annot,type="gtf")

      # create the RnaSeqParam
      rnaSeqParam <- RnaSeqParam(annotParam=annotParam)

      # get a RangedSummarizedExperiment containing the counts table
      sexp <- simpleRNASeq(
        bamFiles=bamFiles,
        param=rnaSeqParam,
        verbose=TRUE
      )

      # get the counts
      assays(sexp)$exons

[Package easyRNASeq version 2.28.0 Index]