SequenceDataFrame-class {RNAmodR} | R Documentation

## The SequenceDataFrame class

### Description

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. To follow the functionallity in the `S4Vectors` package, `SequenceDataFrame` implements the concept, whereas `SequenceDFrame` is the implementation for in-memory data representation from which some specific `*SequenceDataFrame` class derive from, e.g. `CoverageSequenceData`.

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 'SequenceDataFrame'
    cbind(..., deparse.level = 1)

    ## S4 method for signature 'SequenceDataFrame,ANY,ANY,ANY'
    x[i, j, ..., drop = TRUE]

### Arguments

`x, i, j, ..., drop, deparse.level` | arguments used for `subsetting` or `base::cbind`.

### Value

A `SequenceDataFrame` object or if subset to row a `DataFrame`

### Slots

`ranges`

  a `GRanges` object each element describing a transcript including its element. The `GRanges` is constructed from the unlisted results of the `exonsBy(x, by="tx")` function. If during construction a `GRangesList` is provided instead of a character value pointing to a gff3 file or a `TxDb` object, it must have a comparable structure.

`sequence`

  a `XString` of type `sequencesType` from the parent `SequenceData` object.

`condition`

  conditions along the `BamFileList`: Either `control` or `treated`

`replicate`

  replicate number along the `BamFileList` for each of the condition types.

`bamfiles`

  the input bam files as `BamFileList`

`seqinfo`

  a `Seqinfo` describing the avialable/used chromosomes.

### See Also

for an example see `ProtectedEndSequenceData` and for more information see `SequenceData`

### Examples

    data(e5sd,package="RNAmodR")
    # A SequenceDataFrame can is usually constructed by subsetting from
    # a SequenceData object
    sdf <- e5sd[[1]]
    # Its also used to store the unlisted data in a SequenceData object
    sdf <- unlist(e5sd) # should probably only used internally
    e5sd <- relist(sdf,e5sd)

[Package RNAmodR version 1.2.3 Index]