R/SequenceData-protected-end-pos.R
ProtectedEndSequenceData-class.RdProtectedEndSequenceData 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 class 'ProtectedEndSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam'
getData(x, bamfiles, grl, sequences, param, args)
# S4 method for class 'ProtectedEndSequenceData'
aggregateData(x, condition = c("Both", "Treated", "Control"))
# S4 method for class 'ProtectedEndSequenceData'
getDataTrack(x, name, ...)inputs for creating a
SequenceDataFrame. See
SequenceDataFrame.
For aggregate: condition for which the data
should be aggregated.
See
SequenceData and
SequenceData-functions
a ProtectedEndSequenceData
For getDataTrack: a valid
transcript name. Must be a name of ranges(x)
a ProtectedEndSequenceData object
# 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 ...
#> Warning: genome version information is not available for this TxDb object
#> OK
#> Loading protected end data from BAM files ...
#> OK