SequenceData-class {RNAmodR} | R Documentation

## The SequenceData class

### Description

The `SequenceData` class is implemented to contain data on each position along transcripts and holds the corresponding annotation data and nucleotide sequence of these transcripts. To access this data several `functions` are available. The `SequenceData` class is a virtual class, from which specific classes can be extended. Currently the following classes are implemented:

- `CoverageSequenceData`

- `End5SequenceData`, `End3SequenceData`, `EndSequenceData`

- `NormEnd5SequenceData`, `NormEnd5SequenceData`

- `PileupSequenceData`

- `ProtectedEndSequenceData`

The annotation and sequence data can be accessed through the functions `ranges` and `sequences`, respectively. Beaware, that the data is always provided according to genomic positions with increasing `rownames`, but the sequence is given as the actual sequence of the transcript. Therefore, it is necessary to treat the minus strand accordingly.

The `SequenceData` class is derived from the `CompressedSplitDataFrameList` class with additional slots for annotation and sequence data. Some functionality is not inherited and might not available to full extend, e.g.`relist`.

SequenceDataFrame

The `SequenceDataFrame` class is a virtual class and contains data for positions along a single transcript. In addition to being used for returning elements from a `SequenceData` object, the SequenceDataFrame class is used to store the unlisted data within a `SequenceData` object. Therefore, a matching `SequenceData` and `SequenceDataFrame` class must be implemented.

The `SequenceDataFrame` class is derived from the `DataFrame` class.

Subsetting of a `SequenceDataFrame` returns a `SequenceDataFrame` or `DataFrame`, if it is subset by a column or row, respectively. The `drop` argument is ignored for column subsetting.

### Usage

    ## S4 method for signature 'SequenceData'
    cbind(..., deparse.level = 1)

    ## S4 method for signature 'SequenceData'
    rbind(..., deparse.level = 1)

    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'character,character'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'character,BSgenome'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'TxDb,character'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'TxDb,BSgenome'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'GRangesList,character'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'GRangesList,BSgenome'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'GFF3File,BSgenome'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'GFF3File,character'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'character,FaFile'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'GFF3File,FaFile'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'TxDb,FaFile'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

    ## S4 method for signature 'GRangesList,FaFile'
    SequenceData(dataType, bamfiles, annotation, sequences, seqinfo, ...)

### Arguments

`...` | Optional arguments overwriting default values. Not all `SequenceData` classes use all arguments. The arguments are: `minLength` single integer value setting a threshold for minimum read length. Shorther reads are discarded (default: `minLength = NA`). `maxLength` single integer value setting a threshold for maximum read length. Longer reads are discarded (default: `maxLength = NA`). `minQuality` single integer value setting a threshold for maximum read quality. Reads with a lower quality are discarded (default: `minQuality = 5L`, but this is class dependent). `max_depth` maximum depth for pileup loading (default: `max_depth = 10000L`).
`deparse.level` | See `base::cbind` for a description of this argument.
`dataType` | The prefix for construction the class name of the `SequenceData` subclass to be constructed.
`bamfiles` | the input which can be of the following types `BamFileList`: a named `BamFileList` `character`: a `character` vector, which must be coercible to a named `BamFileList` referencing existing bam files. Valid names are `control` and `treated` to define conditions and replicates
`annotation` | annotation data, which must match the information contained in the BAM files.
`sequences` | sequences matching the target sequences the reads were mapped onto. This must match the information contained in the BAM files.
`seqinfo` | optional `Seqinfo` to subset the transcripts analyzed on a chromosome basis.

### Value

A SequenceData object

### Slots

`sequencesType`

  a `character` value for the class name of `sequences`. Either `RNAStringSet`, `ModRNAStringSet`, `DNAStringSet` or `ModDNAStringSet`.

`minQuality`

  a `integer` value describing a threshold of the minimum quality of reads to be used.

[Package RNAmodR version 1.1.15 Index]