EndSequenceData-class {RNAmodR} | R Documentation |
The End5SequenceData
/End3SequenceData
/EndSequenceData
classes aggregate the counts of read ends at each position along a
transcript. End5SequenceData
/End3SequenceData
classes aggregate
either the 5'-end or 3'-end, the EndSequenceData
aggregates both.
All three classes contain one column per data file named using the following
naming convention (end5/end3/end).condition.replicate
.
aggregate
calculates the mean and sd for samples in the control
and treated
condition separatly.
End5SequenceDataFrame( df, ranges, sequence, replicate, condition, bamfiles, seqinfo ) End3SequenceDataFrame( df, ranges, sequence, replicate, condition, bamfiles, seqinfo ) EndSequenceDataFrame( df, ranges, sequence, replicate, condition, bamfiles, seqinfo ) End5SequenceData(bamfiles, annotation, sequences, seqinfo, ...) End3SequenceData(bamfiles, annotation, sequences, seqinfo, ...) EndSequenceData(bamfiles, annotation, sequences, seqinfo, ...) ## S4 method for signature ## 'End5SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam' getData(x, bamfiles, grl, sequences, param, args) ## S4 method for signature ## 'End3SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam' getData(x, bamfiles, grl, sequences, param, args) ## S4 method for signature ## 'EndSequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam' getData(x, bamfiles, grl, sequences, param, args) ## S4 method for signature 'End5SequenceData' aggregateData(x, condition = c("Both", "Treated", "Control")) ## S4 method for signature 'End3SequenceData' aggregateData(x, condition = c("Both", "Treated", "Control")) ## S4 method for signature 'EndSequenceData' aggregateData(x, condition = c("Both", "Treated", "Control")) ## S4 method for signature 'EndSequenceData' getDataTrack(x, name, ...) ## S4 method for signature 'End5SequenceData' getDataTrack(x, name, ...) ## S4 method for signature 'End3SequenceData' 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 End5SequenceData
, a End3SequenceData
or a
EndSequenceData
object
# Construction of a End5SequenceData object 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()) e5sd <- End5SequenceData(files, annotation = annotation, sequences = sequences)