easyRNASeq (version 2.8.2)

simpleRNASeq,BamFileList,RnaSeqParam-method: 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:

• useGenomicAlignmentsfor reading/pre-processing the BAM files.
• get theannotationsdepending on the selected parameters
• calculate the coverage from the provided file(s)
• summarizesthe read counts according to the selected summarization
• returns aRangedSummarizedExperimentobject.

Usage

## S3 method for class '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.

See Also

• For the input:
  • AnnotParam
  • BamParam
  • RnaSeqParam

For the output: RangedSummarizedExperiment For related functions:

• BamFile
• BamFileListgetBamFileList

Examples

## the data
  library("RnaSeqTutorial")

  ## get the BamFileList
  bamFiles <- getBamFileList(
            dir(path=system.file("extdata",
                package="RnaSeqTutorial"),
                pattern="^[A,T].*\\.bam$",
                full.names=TRUE))

  ## create the AnnotParam
  annotParam <- AnnotParam(system.file(
                   "extdata",
                   "Dmel-mRNA-exon-r5.52.gff3",
                   package="RnaSeqTutorial"))

  ## 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
  assay(sexp)$exons