CoverageSequenceData-class {RNAmodR} | R Documentation

## CoverageSequenceData

### Description

`CoverageSequenceData` implements `SequenceData` to contain and aggregate the coverage of reads per position along the transcripts.

`CoverageSequenceData` contains one column per data file named using the following naming convention `coverage.condition.replicate`.

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

### Usage

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

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

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

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

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

### Value

a `CoverageSequenceData` object

### Examples

    # Construction of a CoverageSequenceData objectobject
    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())
    csd <- CoverageSequenceData(files, annotation = annotation,
                                sequences = sequences)

[Package RNAmodR version 1.0.2 Index]