stats {RNAmodR} | R Documentation |
stats
returns information about reads used in the RNAmodR analysis.
Three modes are available depending on which type of object is provided. If a
SequenceData
object is provided, a
BamFile
or
BamFileList
must be provided as well. If a
Modifier
object is used, the bam files
returned from the bamfiles
function are used. This is also the case,
if a ModifierSet
object is used.
stats(x, file, ...) ## S4 method for signature 'SequenceData,BamFile' stats(x, file, ...) ## S4 method for signature 'SequenceData,BamFileList' stats(x, file, ...) ## S4 method for signature 'Modifier,missing' stats(x) ## S4 method for signature 'ModifierSet,missing' stats(x)
x |
a |
file |
a |
... |
optional parameters used as stated
|
a DataFrame
, DataFrameList
or SimpleList
with
the results in aggregated form
library(RNAmodR.Data) library(rtracklayer) sequences <- RNAmodR.Data.example.AAS.fasta() annotation <- GFF3File(RNAmodR.Data.example.AAS.gff3()) files <- list("SampleSet1" = c(treated = RNAmodR.Data.example.wt.1(), treated = RNAmodR.Data.example.wt.2(), treated = RNAmodR.Data.example.wt.3()), "SampleSet2" = c(treated = RNAmodR.Data.example.bud23.1(), treated = RNAmodR.Data.example.bud23.2()), "SampleSet3" = c(treated = RNAmodR.Data.example.trm8.1(), treated = RNAmodR.Data.example.trm8.2())) msi <- ModSetInosine(files, annotation = annotation, sequences = sequences) # smallest chunk of information stats(sequenceData(msi[[1L]]),bamfiles(msi[[1L]])[[1L]]) # partial information stats(sequenceData(msi[[1L]]),bamfiles(msi[[1L]])) # the whole stats stats(msi)