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

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
  library(curl)

# get the example data files - we retrieve a set of example bam files
# from GitHub using curl, as well as their index.
invisible(sapply(c("ACACTG","ACTAGC"),function(bam){
    curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/",
                         "master/tutorial/easyRNASeq/",bam,".bam"),paste0(bam,".bam"))
    curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/",
                         "master/tutorial/easyRNASeq/",bam,".bam.bai"),paste0(bam,".bam.bai"))
  }))

# and some annotation
invisible(curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/",
"master/tutorial/easyRNASeq/Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz"),
"Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz"))

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

  # create the AnnotParam
  annotParam <- AnnotParam("Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz",
                           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