CoverageSequenceData-class: CoverageSequenceData

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

CoverageSequenceData

Description

CoverageSequenceData implements SequenceData to contain and aggregate the coverage of reads per position along the transcripts.

CoverageSequenceData contains one column per data file named using the following naming convention coverage.condition.replicate.

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

Usage

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

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

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

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

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

Value

a CoverageSequenceData object

Examples

# Construction of a CoverageSequenceData objectobject
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())
csd <- CoverageSequenceData(files, annotation = annotation,
                            sequences = sequences)

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