NormEndSequenceData-class: NormEnd5SequenceData/NormEnd3SequenceData

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

Description

The NormEnd5SequenceData/NormEnd3SequenceData aggregate the counts of read ends (Either 5' or 3') at each position along a transcript. In addition, the number of counts are then normalized to the length of the transcript and to the overlapping reads.

Both classes contain three columns per data file named using the following naming convention (normend5/normend3).condition.replicate. The three columns are distinguished by additional identifiers ends, norm.tx and norm.ol.

aggregate calculates the mean and sd for samples in the control and treated condition separatly. Similar to the stored results for each of the two conditions six columns are returned (three for mean and sd each) ending in ends, tx and ol.

Usage

NormEnd5SequenceDataFrame(
  df,
  ranges,
  sequence,
  replicate,
  condition,
  bamfiles,
  seqinfo
)

NormEnd3SequenceDataFrame(
  df,
  ranges,
  sequence,
  replicate,
  condition,
  bamfiles,
  seqinfo
)

NormEnd5SequenceData(bamfiles, annotation, sequences, seqinfo, ...)

NormEnd3SequenceData(bamfiles, annotation, sequences, seqinfo, ...)

## S4 method for signature 
## 'NormEnd5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam'
getData(x, bamfiles, grl, sequences, param, args)

## S4 method for signature 
## 'NormEnd3SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam'
getData(x, bamfiles, grl, sequences, param, args)

## S4 method for signature 'NormEnd5SequenceData'
aggregateData(x, condition = c("Both", "Treated", "Control"))

## S4 method for signature 'NormEnd3SequenceData'
aggregateData(x, condition = c("Both", "Treated", "Control"))

## S4 method for signature 'NormEnd5SequenceData'
getDataTrack(x, name, ...)

## S4 method for signature 'NormEnd3SequenceData'
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 and SequenceData-functions
x	a CoverageSequenceData
name	For getDataTrack: a valid transcript name. Must be a name of ranges(x)

Value

a NormEnd5SequenceData or NormEnd3SequenceData object

Examples

# Construction of a NormEnd5SequenceData object
## Not run: 
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())
ne5sd <- NormEnd5SequenceData(files, annotation = annotation,
                              sequences = sequences)

## End(Not run)

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