NormEndSequenceData-class {RNAmodR} | R Documentation

## NormEnd5SequenceData/NormEnd3SequenceData

### Description

The `NormEnd5SequenceData`/`NormEnd3SequenceData` aggregate the counts of read ends (Either 5' or 3') at each position along a transcript. In addition, the number of counts are then normalized to the length of the transcript and to the overlapping reads.

Both classes contain three columns per data file named using the following naming convention `(normend5/normend3).condition.replicate`. The three columns are distinguished by additional identifiers `ends`, `norm.tx` and `norm.ol`.

`aggregate` calculates the mean and sd for samples in the `control` and `treated` condition separatly. Similar to the stored results for each of the two conditions six columns are returned (three for mean and sd each) ending in `ends`, `tx` and `ol`.

### Usage

    NormEnd5SequenceDataFrame(
      df,
      ranges,
      sequence,
      replicate,
      condition,
      bamfiles,
      seqinfo
    )

    NormEnd3SequenceDataFrame(
      df,
      ranges,
      sequence,
      replicate,
      condition,
      bamfiles,
      seqinfo
    )

    NormEnd5SequenceData(bamfiles, annotation, sequences, seqinfo, ...)

    NormEnd3SequenceData(bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature
    ## 'NormEnd5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam'
    getData(x, bamfiles, grl, sequences, param, args)

    ## S4 method for signature
    ## 'NormEnd3SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam'
    getData(x, bamfiles, grl, sequences, param, args)

    ## S4 method for signature 'NormEnd5SequenceData'
    aggregateData(x, condition = c("Both", "Treated", "Control"))

    ## S4 method for signature 'NormEnd3SequenceData'
    aggregateData(x, condition = c("Both", "Treated", "Control"))

    ## S4 method for signature 'NormEnd5SequenceData'
    getDataTrack(x, name, ...)

    ## S4 method for signature 'NormEnd3SequenceData'
    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 `CoverageSequenceData`
`name` | For `getDataTrack`: a valid transcript name. Must be a name of `ranges(x)`

### Value

a `NormEnd5SequenceData` or `NormEnd3SequenceData` object

### Examples

    # Construction of a NormEnd5SequenceData object
    ## Not run:
    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())
    ne5sd <- NormEnd5SequenceData(files, annotation = annotation,
                                  sequences = sequences)

    ## End(Not run)

[Package RNAmodR version 1.0.2 Index]