Function to generate a variety of feature types from
TxDb objects using
utilities provided by the
GenomicFeatures package. The feature types are
organized per gene and can be returned on that level in their non-reduced or
Currently, supported features include
5'/3'UTR and different
transcript types. The latter contains as many transcript types as
available in the
tx_type column when extracting transcripts from
TxDb objects as follows:
transcripts(txdb, c("tx_name", "gene_id", "tx_type"))
Feature types can be specified by assigning a
If set to
Defines for promoter features the number of bases upstream from the transcription start site.
Defines for promoter features the number of bases downstream from the transcription start site.
The results are returned as a
GRangesList where each component is a
GRanges object containing the range set of each feature type. Intergenic
ranges are assigned unique identifiers and recorded in the
column of the metadata block. For this the ids of their adjacent genes are concatenated with two
underscores as separator. If the adjacent genes overlap with other genes then
their identifiers are included in the id string as well and separated by a single
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## Sample from GenomicFeatures package library(GenomicFeatures) gffFile <- system.file("extdata", "GFF3_files", "a.gff3", package="GenomicFeatures") txdb <- makeTxDbFromGFF(file=gffFile, format="gff3", organism="Solanum lycopersicum") feat <- genFeatures(txdb, featuretype="all", reduce_ranges=FALSE, upstream=1000, downstream=0) ## List extracted feature types names(feat) ## Obtain feature lists by genes, here for promoter split(feat$promoter, unlist(mcols(feat$promoter)$feature_by)) ## Return all features in single GRanges object unlist(feat) ## Not run: ## Sample from systemPipeRdata package file <- system.file("extdata/annotation", "tair10.gff", package="systemPipeRdata") txdb <- makeTxDbFromGFF(file=file, format="gff3", organism="Arabidopsis") feat <- genFeatures(txdb, featuretype="all", reduce_ranges=TRUE, upstream=1000, downstream=0) ## End(Not run)
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