EpiTxDb-class {EpiTxDb} | R Documentation |
The EpiTxDb
class is a
AnnotationDb
type container
for storing Epitranscriptomic information.
The information are typically stored on a per transcript and not as genomic
coordinates, but the EpiTxDb
class is agnostic to this. In case of
genomic coordinates transcriptsBy
will return modifications per
chromosome.
## S4 method for signature 'EpiTxDb' organism(object) ## S4 method for signature 'EpiTxDb' seqinfo(x) ## S4 method for signature 'EpiTxDb' seqlevels(x) ## S4 method for signature 'EpiTxDb' as.list(x)
x, object |
a |
For
organism()
and seqlevels()
a character
vector
seqinfo()
a
Seqinfo
object
as.list()
a list
makeEpiTxDbFromGRanges
for
creating a EpiTxDb
object from a
GRanges
object and it's
metadata columns
makeEpiTxDbFromRMBase
for
creating a EpiTxDb
object from RMBase online resources
makeEpiTxDbFromtRNAdb
for
creating a EpiTxDb
object from tRNAdb online resources
makeEpiTxDb
for creating a
EpiTxDb
object from data.frames
modifications
,
modificationsBy
for getting
epitranscriptomic modification locations
select
for using the default interface of
AnnotationDb
objects.
shiftGenomicToTranscript
and shiftTranscriptToGenomic
for transfering genomic to transcript coordinates and back again.
etdb_file <- system.file("extdata", "EpiTxDb.Hs.hg38.snoRNAdb.sqlite", package="EpiTxDb") etdb <- loadDb(etdb_file) etdb # general methods seqinfo(etdb) # seqlevels(etdb) # easy access to all transcript names