Genomic-Extractors {Organism.dplyr} | R Documentation |
Generic functions to extract genomic features from an object. This
page documents the methods for src_organism
objects
only.
These are the main functions for extracting transcript information
from a src_organism
object, inherited from
transcripts
in
GenomicFeatures
package. Two versions of results are
provided: tibble
(transcripts_tbl()
)
and GRanges
or GRangesList
(transcripts()
).
cds(x, ...) exons(x, ...) genes(x, ...) transcripts(x, ...) cds_tbl(x, filter=NULL, columns=NULL) exons_tbl(x, filter=NULL, columns=NULL) genes_tbl(x, filter=NULL, columns=NULL) transcripts_tbl(x, filter=NULL, columns=NULL) cdsBy(x, by=c("tx", "gene"), ...) exonsBy(x, by=c("tx", "gene"), ...) transcriptsBy(x, by=c("gene", "exon", "cds"), ...) cdsBy_tbl(x, by=c("tx", "gene"), filter=NULL, columns=NULL) exonsBy_tbl(x, by=c("tx", "gene"), filter=NULL, columns=NULL) transcriptsBy_tbl(x, by=c("gene", "exon", "cds"), filter=NULL, columns=NULL) promoters_tbl(x, upstream, downstream, filter=NULL, columns=NULL) intronsByTranscript_tbl(x, filter=NULL, columns=NULL) fiveUTRsByTranscript(x, ...) fiveUTRsByTranscript_tbl(x, filter=NULL, columns=NULL) threeUTRsByTranscript(x, ...) threeUTRsByTranscript_tbl(x, filter=NULL, columns=NULL) ## S4 method for signature 'src_organism' promoters(x, upstream, downstream, filter = NULL, columns = NULL) ## S4 method for signature 'src_organism' intronsByTranscript(x, filter = NULL, columns = NULL)
x |
A |
upstream |
For |
downstream |
For |
filter |
Either NULL, |
columns |
A character vector indicating columns to be included in output
|
by |
One of "gene", "exon", "cds" or "tx". Determines the grouping. |
... |
Additional arguments to S4methods. In this case, the same as
|
functions with _tbl
return a tibble
object, other methods return a GRanges
or
GRangesList
object.
Yubo Cheng.
src_organism
for creating a src_organism
object.
## Not run: src <- src_ucsc("human") src <- src_organism(dbpath=hg38light()) ## transcript coordinates with filter in tibble format filters <- AnnotationFilter(~symbol == c("A1BG", "CDH2")) transcripts_tbl(src, filters) transcripts_tbl(src, AnnotationFilter(~symbol %startsWith% "SNORD")) transcripts_tbl(src, AnnotationFilter(~go == "GO:0005615")) transcripts_tbl(src, filter=AnnotationFilter( ~symbol %startsWith% "SNORD" & tx_start < 25070000)) ## transcript coordinates with filter in granges format filters <- GRangesFilter(GenomicRanges::GRanges("chr15:1-25070000")) transcripts(src, filters) ## promoters promoters(src, upstream=100, downstream=50, filter = SymbolFilter("ADA")) ## transcriptsBy transcriptsBy(src, by = "exon", filter = SymbolFilter("ADA")) ## exonsBy exonsBy(src, filter = SymbolFilter("ADA")) ## intronsByTranscript intronsByTranscript(src, filter = SymbolFilter("ADA"))