R/AllGenerics.R
, R/SequenceDataFrame-class.R
, R/SequenceData-class.R
, and 2 more
SequenceData-functions.Rd
The SequenceData
, SequenceDataSet
, SequenceDataList
and
SequenceDataFrame
classes share functionality. Have a look at the
elements listed directly below.
replicates(x)
# S4 method for SequenceDataFrame
show(object)
# S4 method for SequenceDataFrame
conditions(object)
# S4 method for SequenceDataFrame
bamfiles(x)
# S4 method for SequenceDataFrame
dataType(x)
# S4 method for SequenceDataFrame
ranges(x)
# S4 method for SequenceDataFrame
replicates(x)
# S4 method for SequenceDataFrame
seqinfo(x)
# S4 method for SequenceDataFrame
seqinfo(x)
# S4 method for SequenceDataFrame
seqtype(x)
# S4 method for SequenceDataFrame
seqtype(x) <- value
# S4 method for SequenceDataFrame
sequences(x)
# S4 method for SequenceData
show(object)
# S4 method for SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam
getData(x, bamfiles, grl, sequences, param, args)
# S4 method for SequenceData
bamfiles(x)
# S4 method for SequenceData
conditions(object)
# S4 method for SequenceData
ranges(x)
# S4 method for SequenceData
replicates(x)
# S4 method for SequenceData
seqinfo(x)
# S4 method for SequenceData
sequences(x)
# S4 method for SequenceData
seqtype(x)
# S4 method for SequenceData
seqtype(x) <- value
# S4 method for SequenceData
dataType(x)
# S4 method for SequenceDataSet
show(object)
# S4 method for SequenceDataSet
bamfiles(x)
# S4 method for SequenceDataSet
conditions(object)
# S4 method for SequenceDataSet
names(x)
# S4 method for SequenceDataSet
ranges(x)
# S4 method for SequenceDataSet
replicates(x)
# S4 method for SequenceDataSet
seqinfo(x)
# S4 method for SequenceDataSet
seqtype(x)
# S4 method for SequenceDataSet
seqtype(x) <- value
# S4 method for SequenceDataSet
sequences(x)
# S4 method for SequenceDataList
show(object)
# S4 method for SequenceDataList
bamfiles(x)
# S4 method for SequenceDataList
conditions(object)
# S4 method for SequenceDataList
names(x)
# S4 method for SequenceDataList
ranges(x)
# S4 method for SequenceDataList
replicates(x)
# S4 method for SequenceDataList
seqinfo(x)
# S4 method for SequenceDataList
seqtype(x)
# S4 method for SequenceDataList
seqtype(x) <- value
# S4 method for SequenceDataList
sequences(x)
a SequenceData
, SequenceDataSet
,
SequenceDataList
or a SequenceDataFrame
object.
a new seqtype
, either "RNA" or "DNA"
a BamFileList
.
a GRangesList
from exonsBy(..., by = "tx")
a XStringSet
of type RNAStringSet
,
ModRNAStringSet
, DNAStringSet
or
ModDNAStringSet
a ScanBamParam
object
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)
#> Seqinfo object with 11 sequences from an unspecified genome; no seqlengths:
#> seqnames seqlengths isCircular genome
#> chr1 NA NA <NA>
#> chr2 NA NA <NA>
#> chr3 NA NA <NA>
#> chr4 NA NA <NA>
#> chr5 NA NA <NA>
#> chr6 NA NA <NA>
#> chr7 NA NA <NA>
#> chr8 NA NA <NA>
#> chr9 NA NA <NA>
#> chr10 NA NA <NA>
#> chr11 NA NA <NA>
sequences(e5sd)
#> RNAStringSet object of length 2:
#> width seq names
#> [1] 100 UAUCUGGUUGAUCCUGCCAGUAG...ACAGUGAAACUGCGAAUGGCUCA 1
#> [2] 101 CCGAGAGGUCUUGGUAAUCUUGU...UUCCUAGUAAGCGCAAGUCAUCA 2
ranges(e5sd)
#> GRangesList object of length 2:
#> $`1`
#> GRanges object with 1 range and 3 metadata columns:
#> seqnames ranges strand | exon_id exon_name exon_rank
#> <Rle> <IRanges> <Rle> | <integer> <character> <integer>
#> [1] chr1 1-100 + | 1 rna1 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#> $`2`
#> GRanges object with 1 range and 3 metadata columns:
#> seqnames ranges strand | exon_id exon_name exon_rank
#> <Rle> <IRanges> <Rle> | <integer> <character> <integer>
#> [1] chr1 1500-1600 + | 2 rna2 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
bamfiles(e5sd)
#> BamFileList of length 3
#> names(3): treated treated treated