
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:
GenomicAlignments
for reading/pre-processing the BAM files.annotations
depending on the selected parameterssummarizes
the
read counts according to the selected summarizationRangedSummarizedExperiment
object.## S3 method for class 'BamFileList,RnaSeqParam':
simpleRNASeq(bamFiles = BamFileList(),
param = RnaSeqParam(), nnodes = 1, verbose = TRUE, override = FALSE)
BamFileList
objectRnaSeqParam
object
that describes the RNA-Seq experimental setup.RangedSummarizedExperiment
object.AnnotParam
BamParam
RnaSeqParam
RangedSummarizedExperiment
BamFile
BamFileList
getBamFileList
## 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
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