simpleRNASeq,BamFileList,RnaSeqParam-method {easyRNASeq} | R Documentation |
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.
## S4 method for signature 'BamFileList,RnaSeqParam' simpleRNASeq( bamFiles = BamFileList(), param = RnaSeqParam(), nnodes = 1, verbose = TRUE, override = FALSE )
bamFiles |
a |
param |
RnaSeqParam a |
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 |
returns a RangedSummarizedExperiment
object.
Nicolas Delhomme
For the input:
For the output:
RangedSummarizedExperiment
For related functions:
# 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