ProtectedEndSequenceData-class: ProtectedEndSequenceData

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

ProtectedEndSequenceData

Description

ProtectedEndSequenceData implements SequenceData to contain and aggregate the start and ends of reads per position along a transcript. ProtectedEndSequenceData offsets the start position by -1 to align the information on the 5'-3'-phosphate bonds to one position. The ProtectedEndSequenceData class is implemented specifically as required for the RiboMethSeq method.

The objects of type ProtectedEndSequenceData contain three columns per data file named using the following naming convention protectedend.condition.replicate.

aggregate calculates the mean and sd for samples in the control and treated condition separatly.

Usage

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

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

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

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

## S4 method for signature 'ProtectedEndSequenceData'
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 ProtectedEndSequenceData
name	For getDataTrack: a valid transcript name. Must be a name of ranges(x)

Value

a ProtectedEndSequenceData object

Examples

# Construction of a ProtectedEndSequenceData object
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())
pesd <- ProtectedEndSequenceData(files, annotation = annotation,
                                 sequences = sequences)

FelixErnst/RNAmodR documentation built on March 27, 2024, 2:42 a.m.