Using GRanges defining exons and transcripts, find the splice-junctions
GRanges object with exons and transcripts. A column indicating the position (or rank) of each exon within the transcript must be included.
The column containing the position of each exons within the transcript
The column containing unique transcript-level identifiers
Can be a vector of column names to return beyond rank_col and tx_col. By default all columns are returned (extra_cols = "all").
Length of donor and acceptor sites respectively
Return as a set of GenomicRanges, or with each splice junction annotated as a GenomicInteraction
Not used
A GRanges object with requested columns, and an additional column, 'site', annotating each region as a donor or acceptor site.
Alternatively, by specifying as = "GInteractions", the junctions can be returned with each splice junction annotated as a GenomicInteraction. This can make the set of junctions easier to interpret for a given transcript.
A canonical splice junction consists of a donor site and an acceptor site at each end of an intron, with a branching site somewhere wthin the intron. Canonical donor sites are 8nt long with the the first two bases being exonic and the next 6 being derived form intronic sequences. Canonical acceptor sites are 5nt long with the first four bases being intronic and the final base being the first base of the next exon.
This functions uses each set of exons within a transcript to identify both donor and acceptor sites. Branch sites are not identified.
library(rtracklayer)
gtf_cols <- c(
"transcript_id", "transcript_name", "gene_id", "gene_name", "exon_number"
)
gtf <- import.gff(
system.file("extdata/gencode.v44.subset.gtf.gz", package = "transmogR"),
feature.type = "exon", colnames = gtf_cols
)
sj <- sjFromExons(gtf)
sj
#> GRanges object with 730 ranges and 6 metadata columns:
#> seqnames ranges strand | site transcript_id
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] chr1 182745-182752 + | donor ENST00000624431.2
#> [2] chr1 183128-183132 + | acceptor ENST00000624431.2
#> [3] chr1 183215-183222 + | donor ENST00000624431.2
#> [4] chr1 183490-183494 + | acceptor ENST00000624431.2
#> [5] chr1 183570-183577 + | donor ENST00000624431.2
#> ... ... ... ... . ... ...
#> [726] chr1 810061-810068 - | donor ENST00000590817.3
#> [727] chr1 810170-810174 - | acceptor ENST00000447500.4
#> [728] chr1 817367-817374 - | donor ENST00000447500.4
#> [729] chr1 827664-827671 - | donor ENST00000635509.2
#> [730] chr1 827664-827671 - | donor ENST00000634337.2
#> transcript_name gene_id gene_name exon_number
#> <character> <character> <character> <integer>
#> [1] DDX11L17-201 ENSG00000279928.2 DDX11L17 1
#> [2] DDX11L17-201 ENSG00000279928.2 DDX11L17 2
#> [3] DDX11L17-201 ENSG00000279928.2 DDX11L17 2
#> [4] DDX11L17-201 ENSG00000279928.2 DDX11L17 3
#> [5] DDX11L17-201 ENSG00000279928.2 DDX11L17 3
#> ... ... ... ... ...
#> [726] ENST00000590817 ENSG00000230092.8 ENSG00000230092 1
#> [727] ENST00000447500 ENSG00000290784.1 ENSG00000290784 2
#> [728] ENST00000447500 ENSG00000290784.1 ENSG00000290784 1
#> [729] ENST00000635509 ENSG00000230021.10 ENSG00000230021 1
#> [730] ENST00000634337 ENSG00000230021.10 ENSG00000230021 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Or to simplify shared splice junctions across multiple transcripts
library(extraChIPs, quietly = TRUE)
#> Registered S3 method overwritten by 'ggside':
#> method from
#> +.gg ggplot2
chopMC(sj)
#> GRanges object with 196 ranges and 6 metadata columns:
#> seqnames ranges strand | site
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 182745-182752 + | donor
#> [2] chr1 183128-183132 + | acceptor
#> [3] chr1 183215-183222 + | donor
#> [4] chr1 183490-183494 + | acceptor
#> [5] chr1 183570-183577 + | donor
#> ... ... ... ... . ...
#> [192] chr1 808623-808627 - | acceptor
#> [193] chr1 810061-810068 - | donor
#> [194] chr1 810170-810174 - | acceptor
#> [195] chr1 817367-817374 - | donor
#> [196] chr1 827664-827671 - | donor
#> transcript_id transcript_name
#> <CharacterList> <CharacterList>
#> [1] ENST00000624431.2 DDX11L17-201
#> [2] ENST00000624431.2 DDX11L17-201
#> [3] ENST00000624431.2 DDX11L17-201
#> [4] ENST00000624431.2 DDX11L17-201
#> [5] ENST00000624431.2 DDX11L17-201
#> ... ... ...
#> [192] ENST00000447500.4,ENST00000590817.3 ENST00000447500,ENST00000590817
#> [193] ENST00000447500.4,ENST00000590817.3 ENST00000447500,ENST00000590817
#> [194] ENST00000447500.4 ENST00000447500
#> [195] ENST00000447500.4 ENST00000447500
#> [196] ENST00000635509.2,ENST00000634337.2 ENST00000635509,ENST00000634337
#> gene_id gene_name
#> <CharacterList> <CharacterList>
#> [1] ENSG00000279928.2 DDX11L17
#> [2] ENSG00000279928.2 DDX11L17
#> [3] ENSG00000279928.2 DDX11L17
#> [4] ENSG00000279928.2 DDX11L17
#> [5] ENSG00000279928.2 DDX11L17
#> ... ... ...
#> [192] ENSG00000290784.1,ENSG00000230092.8 ENSG00000290784,ENSG00000230092
#> [193] ENSG00000290784.1,ENSG00000230092.8 ENSG00000290784,ENSG00000230092
#> [194] ENSG00000290784.1 ENSG00000290784
#> [195] ENSG00000290784.1 ENSG00000290784
#> [196] ENSG00000230021.10,ENSG00000230021.10 ENSG00000230021,ENSG00000230021
#> exon_number
#> <IntegerList>
#> [1] 1
#> [2] 2
#> [3] 2
#> [4] 3
#> [5] 3
#> ... ...
#> [192] 3,2
#> [193] 2,1
#> [194] 2
#> [195] 1
#> [196] 1,1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Splice Junctions can also be returned as a GInteractions object with
## anchorOne as the donor & anchorTwo as the acceptor sites
sjFromExons(gtf, as = "GInteractions")
#> GInteractions object with 365 interactions and 5 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 | transcript_id
#> <Rle> <IRanges> <Rle> <IRanges> | <character>
#> [1] chr1 182745-182752 --- chr1 183128-183132 | ENST00000624431.2
#> [2] chr1 183215-183222 --- chr1 183490-183494 | ENST00000624431.2
#> [3] chr1 183570-183577 --- chr1 183736-183740 | ENST00000624431.2
#> [4] chr1 183900-183907 --- chr1 183977-183981 | ENST00000624431.2
#> [5] chr1 724359-724366 --- chr1 724714-724718 | ENST00000440782.3
#> ... ... ... ... ... ... . ...
#> [361] chr1 817367-817374 --- chr1 774280-774284 | ENST00000447500.4
#> [362] chr1 827664-827671 --- chr1 801163-801167 | ENST00000635509.2
#> [363] chr1 827664-827671 --- chr1 805891-805895 | ENST00000634337.2
#> [364] chr1 720026-720033 --- chr1 805891-805895 | ENST00000414688.6
#> [365] chr1 711705-711712 --- chr1 808623-808627 | ENST00000635509.2
#> transcript_name gene_id gene_name sj
#> <character> <character> <character> <integer>
#> [1] DDX11L17-201 ENSG00000279928.2 DDX11L17 1
#> [2] DDX11L17-201 ENSG00000279928.2 DDX11L17 2
#> [3] DDX11L17-201 ENSG00000279928.2 DDX11L17 3
#> [4] DDX11L17-201 ENSG00000279928.2 DDX11L17 4
#> [5] CICP3-201 ENSG00000229376.3 CICP3 1
#> ... ... ... ... ...
#> [361] ENST00000447500 ENSG00000290784.1 ENSG00000290784 1
#> [362] ENST00000635509 ENSG00000230021.10 ENSG00000230021 1
#> [363] ENST00000634337 ENSG00000230021.10 ENSG00000230021 1
#> [364] ENST00000414688 ENSG00000230021.10 ENSG00000230021 2
#> [365] ENST00000635509 ENSG00000230021.10 ENSG00000230021 2
#> -------
#> regions: 196 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths