PileupSequenceData-class {RNAmodR} | R Documentation

## PileupSequenceData

### Description

The `PileupSequenceData` aggregates the pileup of called bases per position.

`PileupSequenceData` contains five columns per data file named using the following naming convention `pileup.condition.replicate`. The five columns are distinguished by additional identifiers `-`, `G`, `A`, `T` and `C`.

`aggregate` calculates the mean and sd for each nucleotide in the `control` and `treated` condition separatly. The results are then normalized to a row sum of 1.

### Usage

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

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

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

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

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

    pileupToCoverage(x)

    ## S4 method for signature 'PileupSequenceData'
    pileupToCoverage(x)

### 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 `PileupSequenceData`
`name` | For `getDataTrack`: a valid transcript name. Must be a name of `ranges(x)`

### Value

a `PileupSequenceData` object

### Examples

    # Construction of a PileupSequenceData 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())
    psd <- PileupSequenceData(files, annotation = annotation,
                              sequences = sequences)

[Package RNAmodR version 1.2.3 Index]