ProtectedEndSequenceData-class {RNAmodR} | R Documentation

## ProtectedEndSequenceData

### Description

`ProtectedEndSequenceData` implements `SequenceData` to contain and aggregate the start and ends of reads per position along a transcript. `ProtectedEndSequenceData` offsets the start position by -1 to align the information on the 5'-3'-phosphate bonds to one position. The `ProtectedEndSequenceData` class is implemented specifically as required for the `RiboMethSeq` method.

The objects of type `ProtectedEndSequenceData` contain three columns per data file named using the following naming convention `protectedend.condition.replicate`.

`aggregate` calculates the mean and sd for samples in the `control` and `treated` condition separatly.

### Usage

    ProtectedEndSequenceDataFrame(
      df,
      ranges,
      sequence,
      replicate,
      condition,
      bamfiles,
      seqinfo
    )

    ProtectedEndSequenceData(bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature
    ## 'ProtectedEndSequenceData,
    ##   BamFileList,
    ##   GRangesList,
    ##   XStringSet,
    ##   ScanBamParam'
    getData(x, bamfiles, grl, sequences, param, args)

    ## S4 method for signature 'ProtectedEndSequenceData'
    aggregateData(x, condition = c("Both", "Treated", "Control"))

    ## S4 method for signature 'ProtectedEndSequenceData'
    getDataTrack(x, name, ...)

### Arguments

`df, ranges, sequence, replicate` | inputs for creating a `SequenceDataFrame`. See `SequenceDataFrame`.
`condition` | For `aggregate`: condition for which the data should be aggregated.
`bamfiles, annotation, seqinfo, grl, sequences, param, args, ...` | See `SequenceData` and `SequenceData-functions`
`x` | a `ProtectedEndSequenceData`
`name` | For `getDataTrack`: a valid transcript name. Must be a name of `ranges(x)`

### Value

a `ProtectedEndSequenceData` object

### Examples

    # Construction of a ProtectedEndSequenceData 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())
    pesd <- ProtectedEndSequenceData(files, annotation = annotation,
                                     sequences = sequences)

[Package RNAmodR version 1.2.3 Index]