The PileupSequenceData aggregates the pileup of called bases per
position.
PileupSequenceData contains five columns per data file named using the
following naming convention pileup.condition.replicate. The five
columns are distinguished by additional identifiers -, G,
A, T and C.
aggregate calculates the mean and sd for each nucleotide in the
control and treated condition separatly. The results are then
normalized to a row sum of 1.
PileupSequenceDataFrame(
df,
ranges,
sequence,
replicate,
condition,
bamfiles,
seqinfo
)
PileupSequenceData(bamfiles, annotation, sequences, seqinfo, ...)
# S4 method for class 'PileupSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam'
getData(x, bamfiles, grl, sequences, param, args)
# S4 method for class 'PileupSequenceData'
aggregateData(x, condition = c("Both", "Treated", "Control"))
# S4 method for class 'PileupSequenceData'
getDataTrack(x, name, ...)
pileupToCoverage(x)
# S4 method for class 'PileupSequenceData'
pileupToCoverage(x)inputs for creating a
SequenceDataFrame. See
SequenceDataFrame.
For aggregate: condition for which the data
should be aggregated.
See
SequenceData and
SequenceData-functions
a PileupSequenceData
For getDataTrack: a valid
transcript name. Must be a name of ranges(x)
a PileupSequenceData object
# Construction of a PileupSequenceData 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
psd <- PileupSequenceData(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 Pileup data from BAM files ...
#> OK