stats {RNAmodR} | R Documentation

## Retrieving information about used reads in RNAmodR

### 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)

[Package RNAmodR version 1.2.3 Index]