Genomic-Extractors {Organism.dplyr} | R Documentation

## Extract genomic features from src_organism objects

### Description

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()`).

### Usage

    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)

### Arguments

`x` | A `src_organism` object
`upstream` | For `promoters()`: An integer(1) value indicating the number of bases upstream from the transcription start site.
`downstream` | For `promoters()`: An integer(1) value indicating the number of bases downstream from the transcription start site.
`filter` | Either NULL, `AnnotationFilter`, or `AnnotationFilterList` to be used to restrict the output. Filters consists of `AnnotationFilter`s and can be a `GRanges` object using "GRangesFilter" (see examples).
`columns` | A character vector indicating columns to be included in output `GRanges` object or `tbl`.
`by` | One of "gene", "exon", "cds" or "tx". Determines the grouping.
`...` | Additional arguments to S4methods. In this case, the same as `filter`.

### Value

functions with `_tbl` return a `tibble` object, other methods return a `GRanges` or `GRangesList` object.

### Author(s)

Yubo Cheng.

### See Also

`src_organism` for creating a `src_organism` object.

### Examples

    ## 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"))

    ## fiveUTRsByTranscript
    fiveUTRsByTranscript(src, filter = SymbolFilter("ADA"))

[Package Organism.dplyr version 1.6.2 Index]