SequenceData-functions {RNAmodR} | R Documentation

## SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame functions

### Description

The `SequenceData`, `SequenceDataSet`, `SequenceDataList` and `SequenceDataFrame` classes share functionality. Have a look at the elements listed directly below.

### Usage

    replicates(x)

    ## S4 method for signature 'SequenceDataFrame'
    show(object)

    ## S4 method for signature 'SequenceDataFrame'
    conditions(object)

    ## S4 method for signature 'SequenceDataFrame'
    bamfiles(x)

    ## S4 method for signature 'SequenceDataFrame'
    dataType(x)

    ## S4 method for signature 'SequenceDataFrame'
    ranges(x)

    ## S4 method for signature 'SequenceDataFrame'
    replicates(x)

    ## S4 method for signature 'SequenceDataFrame'
    seqinfo(x)

    ## S4 method for signature 'SequenceDataFrame'
    seqinfo(x)

    ## S4 method for signature 'SequenceDataFrame'
    seqtype(x)

    ## S4 replacement method for signature 'SequenceDataFrame'
    seqtype(x) <- value

    ## S4 method for signature 'SequenceDataFrame'
    sequences(x)

    ## S4 method for signature 'SequenceData'
    show(object)

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

    ## S4 method for signature 'SequenceData'
    bamfiles(x)

    ## S4 method for signature 'SequenceData'
    conditions(object)

    ## S4 method for signature 'SequenceData'
    ranges(x)

    ## S4 method for signature 'SequenceData'
    replicates(x)

    ## S4 method for signature 'SequenceData'
    seqinfo(x)

    ## S4 method for signature 'SequenceData'
    sequences(x)

    ## S4 method for signature 'SequenceData'
    seqtype(x)

    ## S4 replacement method for signature 'SequenceData'
    seqtype(x) <- value

    ## S4 method for signature 'SequenceData'
    dataType(x)

    ## S4 method for signature 'SequenceDataSet'
    show(object)

    ## S4 method for signature 'SequenceDataSet'
    bamfiles(x)

    ## S4 method for signature 'SequenceDataSet'
    conditions(object)

    ## S4 method for signature 'SequenceDataSet'
    names(x)

    ## S4 method for signature 'SequenceDataSet'
    ranges(x)

    ## S4 method for signature 'SequenceDataSet'
    replicates(x)

    ## S4 method for signature 'SequenceDataSet'
    seqinfo(x)

    ## S4 method for signature 'SequenceDataSet'
    seqtype(x)

    ## S4 replacement method for signature 'SequenceDataSet'
    seqtype(x) <- value

    ## S4 method for signature 'SequenceDataSet'
    sequences(x)

    ## S4 method for signature 'SequenceDataList'
    show(object)

    ## S4 method for signature 'SequenceDataList'
    bamfiles(x)

    ## S4 method for signature 'SequenceDataList'
    conditions(object)

    ## S4 method for signature 'SequenceDataList'
    names(x)

    ## S4 method for signature 'SequenceDataList'
    ranges(x)

    ## S4 method for signature 'SequenceDataList'
    replicates(x)

    ## S4 method for signature 'SequenceDataList'
    seqinfo(x)

    ## S4 method for signature 'SequenceDataList'
    seqtype(x)

    ## S4 replacement method for signature 'SequenceDataList'
    seqtype(x) <- value

    ## S4 method for signature 'SequenceDataList'
    sequences(x)

### Arguments

`x, object` | a `SequenceData`, `SequenceDataSet`, `SequenceDataList` or a `SequenceDataFrame` object.
`value` | a new `seqtype`, either "RNA" or "DNA"
`bamfiles` | a `BamFileList`.
`grl` | a `GRangesList` from `exonsBy(..., by = "tx")`
`sequences` | a `XStringSet` of type `RNAStringSet`, `ModRNAStringSet`, `DNAStringSet` or `ModDNAStringSet`
`param` | a `ScanBamParam` object
`args` | a list of addition arguments

### Value

- `seqinfo`: a `Seqinfo` object ().

- `sequences`: a `RNAStingSet` object or a `RNAString` object for a `SequenceDataFrame`.

- `ranges`: a `GRangesList` object with each element per transcript or a `GRanges` object for a `SequenceDataFrame`.

- `bamfiles`: a `BamFileList` object or a SimpleList of `BamFileList` objects for a `SequenceDataList`.

### Examples

    data(e5sd,package="RNAmodR")
    # general accessors
    seqinfo(e5sd)
    sequences(e5sd)
    ranges(e5sd)
    bamfiles(e5sd)

[Package RNAmodR version 1.2.3 Index]