stats: Retrieving information about used reads in RNAmodR

In RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data

Description

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.

Usage

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)

Arguments

x	a SequenceData, Modifier or ModifierSet object
file	a BamFile or BamFileList, if x is a SequenceData object.
...	optional parameters used as stated here (except minQuality), if x is a SequenceData object.

Value

a DataFrame, DataFrameList or SimpleList with the results in aggregated form

Examples

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)

RNAmodR documentation built on Dec. 15, 2020, 2 a.m.