EndSequenceData-class {RNAmodR} | R Documentation

## End5SequenceData/End3SequenceData/EndSequenceData

### Description

The `End5SequenceData`/`End3SequenceData`/`EndSequenceData` classes aggregate the counts of read ends at each position along a transcript. `End5SequenceData`/`End3SequenceData` classes aggregate either the 5'-end or 3'-end, the `EndSequenceData` aggregates both.

All three classes contain one column per data file named using the following naming convention `(end5/end3/end).condition.replicate`.

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

### Usage

    End5SequenceDataFrame(
      df,
      ranges,
      sequence,
      replicate,
      condition,
      bamfiles,
      seqinfo
    )

    End3SequenceDataFrame(
      df,
      ranges,
      sequence,
      replicate,
      condition,
      bamfiles,
      seqinfo
    )

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

    End5SequenceData(bamfiles, annotation, sequences, seqinfo, ...)

    End3SequenceData(bamfiles, annotation, sequences, seqinfo, ...)

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

    ## S4 method for signature
    ## 'End5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam'
    getData(x, bamfiles, grl, sequences, param, args)

    ## S4 method for signature
    ## 'End3SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam'
    getData(x, bamfiles, grl, sequences, param, args)

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

    ## S4 method for signature 'End5SequenceData'
    aggregateData(x, condition = c("Both", "Treated", "Control"))

    ## S4 method for signature 'End3SequenceData'
    aggregateData(x, condition = c("Both", "Treated", "Control"))

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

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

    ## S4 method for signature 'End5SequenceData'
    getDataTrack(x, name, ...)

    ## S4 method for signature 'End3SequenceData'
    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 `End5SequenceData`, `End3SequenceData` or `EndSequenceData` object
`name` | For `getDataTrack`: a valid transcript name. Must be a name of `ranges(x).`

### Value

a `End5SequenceData`, a `End3SequenceData` or a `EndSequenceData` object

### Examples

    # Construction of a End5SequenceData 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())
    e5sd <- End5SequenceData(files, annotation = annotation,
                            sequences = sequences)

[Package RNAmodR version 1.4.2 Index]