Table-based helper returning one row per exon for the transcripts of the
requested genes, joined with transcript and gene attributes. This is the
input format of the data-frame method of plot_genomic_context().
With an IsoformicExperiment use exon_table() instead.
Usage
prepare_exon_annotation(
gene_name,
file_path,
file_type = c("auto", "gff", "gtf"),
output_path = NULL
)Arguments
- gene_name
Character vector of gene names (or gene IDs).
- file_path
Path to an annotation directory or a GFF3/GTF file.
- file_type
Passed to
prepare_isoformic_annotation().- output_path
Passed to
prepare_isoformic_annotation().
Value
A tibble with columns gene_id, gene_name, transcript_id,
transcript_name, transcript_type, exon_id, exon_number, seqid,
start_pos, end_pos, strand.
Examples
gff <- system.file("extdata", "example.gff3", package = "isoformic")
exons <- prepare_exon_annotation("RBPJ", gff, output_path = tempdir())
#> ℹ Using cached annotation directory /tmp/RtmpV2WK1u/example.
head(exons)
#> # A tibble: 6 × 12
#> gene_id gene_name transcript_id transcript_name transcript_type haplotype
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 2 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 3 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 4 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 5 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> 6 ENSG0000016… RBPJ ENST00000342… RBPJ-201 protein_coding NA
#> # ℹ 6 more variables: exon_id <chr>, exon_number <int>, seqid <chr>,
#> # start_pos <int>, end_pos <int>, strand <chr>