exonicParts {GenomicFeatures} | R Documentation

## Extract non-overlapping exonic or intronic parts from a TxDb-like object

### Description

`exonicParts` and `intronicParts` extract the non-overlapping (a.k.a. disjoint) exonic or intronic parts from a TxDb-like object.

### Usage

    exonicParts(txdb, linked.to.single.gene.only=FALSE)
    intronicParts(txdb, linked.to.single.gene.only=FALSE)

    ## 3 helper functions used internally by exonicParts() and intronicParts():
    tidyTranscripts(txdb, drop.geneless=FALSE)
    tidyExons(txdb, drop.geneless=FALSE)
    tidyIntrons(txdb, drop.geneless=FALSE)

### Arguments

`txdb` | A TxDb object, or any TxDb-like object that supports the `transcripts()` and `exonsBy()` extractors (e.g. an EnsDb object).
`linked.to.single.gene.only` | `TRUE` or `FALSE`. If `FALSE` (the default), then the disjoint parts are obtained by calling `disjoin()` on all the exons (or introns) in `txdb`, including on exons (or introns) not linked to a gene or linked to more than one gene. If `TRUE`, then the disjoint parts are obtained in 2 steps: call `disjoin()` on the exons (or introns) linked to at least one gene, then drop the parts linked to more than one gene from the set of exonic (or intronic) parts obtained previously.
`drop.geneless` | If `FALSE` (the default), then all the transcripts (or exons, or introns) get extracted from the TxDb object. If `TRUE`, then only the transcripts (or exons, or introns) that are linked to a gene get extracted from the TxDb object. Note that `drop.geneless` also impacts the order in which the features are returned: Transcripts: If `drop.geneless` is `FALSE` then transcripts are returned in the same order as with `transcripts`, which is expected to be by internal transcript id (`tx_id`). Otherwise they are ordered first by gene id (`gene_id`), then by internal transcript id. Exons: If `drop.geneless` is `FALSE` then exons are ordered first by internal transcript id (`tx_id`), then by exon rank (`exon_rank`). Otherwise they are ordered first by gene id (`gene_id`), then by internal transcript id, and then by exon rank. Introns: If `drop.geneless` is `FALSE` then introns are ordered by internal transcript id (`tx_id`). Otherwise they are ordered first by gene id (`gene_id`), then by internal transcript id.

### Value

`exonicParts` returns a disjoint and strictly sorted GRanges object with 1 range per exonic part and with metadata columns `tx_id`, `tx_name`, `gene_id`, `exon_id`, `exon_name`, and `exon_rank`. If `linked.to.single.gene.only` was set to `TRUE`, an additional `exonic_part` metadata column is added that indicates the rank of each exonic part within all the exonic parts linked to the same gene.

`intronicParts` returns a disjoint and strictly sorted GRanges object with 1 range per intronic part and with metadata columns `tx_id`, `tx_name`, and `gene_id`. If `linked.to.single.gene.only` was set to `TRUE`, an additional `intronic_part` metadata column is added that indicates the rank of each intronic part within all the intronic parts linked to the same gene.

`tidyTranscripts` returns a GRanges object with 1 range per transcript and with metadata columns `tx_id`, `tx_name`, and `gene_id`.

`tidyExons` returns a GRanges object with 1 range per exon and with metadata columns `tx_id`, `tx_name`, `gene_id`, `exon_id`, `exon_name`, and `exon_rank`.

`tidyIntrons` returns a GRanges object with 1 range per intron and with metadata columns `tx_id`, `tx_name`, and `gene_id`.

### Note

`exonicParts` is a replacement for `disjointExons` with the following differences/improvements:

- Argument `linked.to.single.gene.only` in `exonicParts` replaces argument `aggregateGenes` in `disjointExons`, but has opposite meaning i.e. `exonicParts(txdb, linked.to.single.gene.only=TRUE)` returns the same exonic parts as `disjointExons(txdb, aggregateGenes=FALSE)`.

- Unlike `disjointExons(txdb, aggregateGenes=TRUE)`, `exonicParts(txdb, linked.to.single.gene.only=FALSE)` does NOT discard exon parts that are not linked to a gene.

- `exonicParts` is almost 2x more efficient than `disjointExons`.

- `exonicParts` works out-of-the-box on any TxDb-like object that supports the `transcripts()` and `exonsBy()` extractors (e.g. on an EnsDb object).

### Author(s)

Hervé Pagès

### See Also

- `disjoin` in the IRanges package.

- `transcripts`, `transcriptsBy`, and `transcriptsByOverlaps`, for extracting genomic feature locations from a TxDb-like object.

- `transcriptLengths` for extracting the transcript lengths (and other metrics) from a TxDb object.

- `extractTranscriptSeqs` for extracting transcript (or CDS) sequences from chromosome sequences.

- `coverageByTranscript` for computing coverage by transcript (or CDS) of a set of ranges.

- The TxDb class.

### Examples

    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

    ## ---------------------------------------------------------------------
    ## exonicParts()
    ## ---------------------------------------------------------------------

    exonic_parts1 <- exonicParts(txdb)
    exonic_parts1

    ## Mapping from exonic parts to genes is many-to-many:
    gene_id1 <- mcols(exonic_parts1)$gene_id
    gene_id1  # CharacterList object
    table(lengths(gene_id1))
    ## The number of known genes a Human exonic part can be linked to
    ## varies from 0 to 22!

    exonic_parts2 <- exonicParts(txdb, linked.to.single.gene.only=TRUE)
    exonic_parts2

    ## Mapping from exonic parts to genes now is many-to-one:
    gene_id2 <- mcols(exonic_parts2)$gene_id
    gene_id2[1:20]  # character vector

    ## Select exonic parts for a given gene:
    exonic_parts2[gene_id2 %in% "643837"]

    ## Sanity checks:
    stopifnot(isDisjoint(exonic_parts1), isStrictlySorted(exonic_parts1))
    stopifnot(isDisjoint(exonic_parts2), isStrictlySorted(exonic_parts2))
    stopifnot(all(exonic_parts2 %within% reduce(exonic_parts1)))
    stopifnot(identical(
        lengths(gene_id1) == 1L,
        exonic_parts1 %within% exonic_parts2
    ))

    ## ---------------------------------------------------------------------
    ## intronicParts()
    ## ---------------------------------------------------------------------

    intronic_parts1 <- intronicParts(txdb)
    intronic_parts1

    ## Mapping from intronic parts to genes is many-to-many:
    mcols(intronic_parts1)$gene_id
    table(lengths(mcols(intronic_parts1)$gene_id))
    ## A Human intronic part can be linked to 0 to 22 known genes!

    intronic_parts2 <- intronicParts(txdb, linked.to.single.gene.only=TRUE)
    intronic_parts2

    ## Mapping from intronic parts to genes now is many-to-one:
    class(mcols(intronic_parts2)$gene_id)  # character vector

    ## Sanity checks:
    stopifnot(isDisjoint(intronic_parts1), isStrictlySorted(intronic_parts1))
    stopifnot(isDisjoint(intronic_parts2), isStrictlySorted(intronic_parts2))
    stopifnot(all(intronic_parts2 %within% reduce(intronic_parts1)))
    stopifnot(identical(
        lengths(mcols(intronic_parts1)$gene_id) == 1L,
        intronic_parts1 %within% intronic_parts2
    ))

    ## ---------------------------------------------------------------------
    ## Helper functions
    ## ---------------------------------------------------------------------

    tidyTranscripts(txdb)                      # Ordered by 'tx_id'.
    tidyTranscripts(txdb, drop.geneless=TRUE)  # Ordered first by 'gene_id',
                                               # then by 'tx_id'.

    tidyExons(txdb)                            # Ordered first by 'tx_id',
                                               # then by 'exon_rank'.
    tidyExons(txdb, drop.geneless=TRUE)        # Ordered first by 'gene_id',
                                               # then by 'tx_id',
                                               # then by 'exon_rank'.

    tidyIntrons(txdb)                          # Ordered by 'tx_id'.
    tidyIntrons(txdb, drop.geneless=TRUE)      # Ordered first by 'gene_id',
                                               # then by 'tx_id'.

[Package GenomicFeatures version 1.40.1 Index]