ProtectedEndSequenceData

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.

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

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

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

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

# S4 method for 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())
#> see ?RNAmodR.Data and browseVignettes('RNAmodR.Data') for documentation
#> loading from cache
sequences <- RNAmodR.Data.example.man.fasta()
#> see ?RNAmodR.Data and browseVignettes('RNAmodR.Data') for documentation
#> loading from cache
files <- c(treated = RNAmodR.Data.example.wt.1())
#> see ?RNAmodR.Data and browseVignettes('RNAmodR.Data') for documentation
#> loading from cache
pesd <- ProtectedEndSequenceData(files, annotation = annotation,
                                 sequences = sequences)
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK
#> Loading protected end data from BAM files ... 
#> OK