SequenceData-functions {RNAmodR} | R Documentation |
The SequenceData
, SequenceDataSet
, SequenceDataList
and
SequenceDataFrame
classes share functionality. Have a look at the
elements listed directly below.
replicates(x) ## S4 method for signature 'SequenceDataFrame' show(object) ## S4 method for signature 'SequenceDataFrame' conditions(object) ## S4 method for signature 'SequenceDataFrame' bamfiles(x) ## S4 method for signature 'SequenceDataFrame' dataType(x) ## S4 method for signature 'SequenceDataFrame' ranges(x) ## S4 method for signature 'SequenceDataFrame' replicates(x) ## S4 method for signature 'SequenceDataFrame' seqinfo(x) ## S4 method for signature 'SequenceDataFrame' seqinfo(x) ## S4 method for signature 'SequenceDataFrame' seqtype(x) ## S4 replacement method for signature 'SequenceDataFrame' seqtype(x) <- value ## S4 method for signature 'SequenceDataFrame' sequences(x) ## S4 method for signature 'SequenceData' show(object) ## S4 method for signature ## 'SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam' getData(x, bamfiles, grl, sequences, param, args) ## S4 method for signature 'SequenceData' bamfiles(x) ## S4 method for signature 'SequenceData' conditions(object) ## S4 method for signature 'SequenceData' ranges(x) ## S4 method for signature 'SequenceData' replicates(x) ## S4 method for signature 'SequenceData' seqinfo(x) ## S4 method for signature 'SequenceData' sequences(x) ## S4 method for signature 'SequenceData' seqtype(x) ## S4 replacement method for signature 'SequenceData' seqtype(x) <- value ## S4 method for signature 'SequenceData' dataType(x) ## S4 method for signature 'SequenceDataSet' show(object) ## S4 method for signature 'SequenceDataSet' bamfiles(x) ## S4 method for signature 'SequenceDataSet' conditions(object) ## S4 method for signature 'SequenceDataSet' names(x) ## S4 method for signature 'SequenceDataSet' ranges(x) ## S4 method for signature 'SequenceDataSet' replicates(x) ## S4 method for signature 'SequenceDataSet' seqinfo(x) ## S4 method for signature 'SequenceDataSet' seqtype(x) ## S4 replacement method for signature 'SequenceDataSet' seqtype(x) <- value ## S4 method for signature 'SequenceDataSet' sequences(x) ## S4 method for signature 'SequenceDataList' show(object) ## S4 method for signature 'SequenceDataList' bamfiles(x) ## S4 method for signature 'SequenceDataList' conditions(object) ## S4 method for signature 'SequenceDataList' names(x) ## S4 method for signature 'SequenceDataList' ranges(x) ## S4 method for signature 'SequenceDataList' replicates(x) ## S4 method for signature 'SequenceDataList' seqinfo(x) ## S4 method for signature 'SequenceDataList' seqtype(x) ## S4 replacement method for signature 'SequenceDataList' seqtype(x) <- value ## S4 method for signature 'SequenceDataList' sequences(x)
x, object |
a |
value |
a new |
bamfiles |
a |
grl |
a |
sequences |
a |
param |
a |
args |
a list of addition arguments |
seqinfo
: a Seqinfo
object ().
sequences
: a RNAStingSet
object or a RNAString
object for a SequenceDataFrame
.
ranges
: a GRangesList
object with each element per
transcript or a GRanges
object for a SequenceDataFrame
.
bamfiles
: a BamFileList
object or a SimpleList of
BamFileList
objects for a SequenceDataList
.
data(e5sd,package="RNAmodR") # general accessors seqinfo(e5sd) sequences(e5sd) ranges(e5sd) bamfiles(e5sd)