SequenceData-functions: SequenceData/SequenceDataSet/SequenceDataList/SequenceDataFrame...

In RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data

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)

RNAmodR documentation built on Dec. 15, 2020, 2 a.m.