ModInosine {RNAmodR} | R Documentation

## ModInosine

### Description

Inosine can be detected in RNA-Seq data by the conversion of A positions to G. This conversion is detected by `ModInosine` and used to search for Inosine positions. `dataType` is `"PileupSequenceData"`.

Only samples labeled with the condition `treated` are used for this analysis, since the A to G conversion is common feature among the reverse transcriptases usually emploied. Let us know, if that is not the case, and the class needs to be modified.

Further information on `Functions` of `ModInosine`.

### Usage

    ModInosine(x, annotation, sequences, seqinfo, ...)

    ModSetInosine(x, annotation = NA, sequences = NA, seqinfo = NA, ...)

### Arguments

`x` | the input which can be of the different types depending on whether a `ModRiboMethSeq` or a `ModSetRiboMethSeq` object is to be constructed. For more information have a look at the documentation of the `Modifier` and `ModifierSet` classes.
`annotation` | annotation data, which must match the information contained in the BAM files. This is parameter is only required, if `x` is not a `Modifier` object.
`sequences` | sequences matching the target sequences the reads were mapped onto. This must match the information contained in the BAM files. This is parameter is only required, if `x` is not a `Modifier` object.
`seqinfo` | An optional `Seqinfo` argument or character vector, which can be coerced to one, to subset the sequences to be analyzed on a per chromosome basis.
`...` | Optional arguments overwriting default values, which are minCoverage: The minimal coverage at the position as integer value (default: `minCoverage = 10L`). minReplicate: minimum number of replicates needed for the analysis (default: `minReplicate = 1L`). minScore: minimum score to identify Inosine positions de novo (default: `minScore = 0.4`).

### Details

`ModInosine` score: the scores for reported Inosine positions are between 0 and 1. They are calculated as the relative amount of called G bases (`(G / N)`) and only saved for genomic A positions.

### Value

a `ModInosine` or `ModSetInosine` object

### Author(s)

Felix G.M. Ernst [aut]

### Examples

    # construction of ModInosine object
    library(RNAmodR.Data)
    library(rtracklayer)
    annotation <- GFF3File(RNAmodR.Data.example.man.gff3())
    sequences <- RNAmodR.Data.example.man.fasta()
    files <- c(treated = RNAmodR.Data.example.wt.1())
    mi <- ModInosine(files,annotation = annotation ,sequences = sequences)
    # construction of ModSetInosine object
    ## Not run:
    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)

    ## End(Not run)

[Package RNAmodR version 1.2.3 Index]