CoverageSequenceData-class {RNAmodR} | R Documentation |
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.
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, ...)
df, ranges, sequence, replicate |
inputs for creating a
|
condition |
For |
bamfiles, annotation, seqinfo, grl, sequences, param, args, ... |
See
|
x |
a |
name |
For |
a CoverageSequenceData
object
# 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)