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Tiny example GTF files

Source: R/example_gtf.R
tiny_example_gtf_files.Rd

These are minimal GTF files used for examples and testing within the package.

  • gencode.v1.example.gtf.gz contains two genes:

    • GeneA: a single-exon, unspliced gene.

    • GeneB: a spliced gene with two transcripts and multiple exons.

  • gencode.v2.example.gtf.gz contains the same two genes as in gencode.v1.example.gtf.gz plus:

    • GeneC: a new spliced gene with multiple transcripts and many exons.

These files are stored in the inst/extdata/ directory and can be accessed using system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2") or system.file("extdata", "gencode.v2.example.gtf.gz", package = "GencoDymo2").

Format

Two external GTF files.

Source

Generated manually for testing purposes.

See also

load_file

Examples

tiny_v1_path <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
tiny_v2_path <- system.file("extdata", "gencode.v2.example.gtf.gz", package = "GencoDymo2")

gtf1 <- load_file(tiny_v1_path)
head(gtf1)
#>   seqnames start   end width strand source       type score phase gene_id
#> 1     chr1  1000  5000  4001      + HAVANA       gene    NA    NA   GeneA
#> 2     chr1  1000  5000  4001      + HAVANA transcript    NA    NA   GeneA
#> 3     chr1  1000  5000  4001      + HAVANA       exon    NA    NA   GeneA
#> 4     chr1  6000 12000  6001      - HAVANA       gene    NA    NA   GeneB
#> 5     chr1  6000 12000  6001      - HAVANA transcript    NA    NA   GeneB
#> 6     chr1  6000  6500   501      - HAVANA       exon    NA    NA   GeneB
#>       gene_name transcript_id exon_number
#> 1 UnsplicedGene          <NA>        <NA>
#> 2          <NA>     GeneA-001        <NA>
#> 3          <NA>     GeneA-001           1
#> 4   SplicedGene          <NA>        <NA>
#> 5          <NA>     GeneB-001        <NA>
#> 6          <NA>     GeneB-001           1

gtf2 <- load_file(tiny_v2_path)
head(gtf2)
#>   seqnames start   end width strand source       type score phase gene_id
#> 1     chr1  1000  5000  4001      + HAVANA       gene    NA    NA   GeneA
#> 2     chr1  1000  5000  4001      + HAVANA transcript    NA    NA   GeneA
#> 3     chr1  1000  5000  4001      + HAVANA       exon    NA    NA   GeneA
#> 4     chr1  6000 12000  6001      - HAVANA       gene    NA    NA   GeneB
#> 5     chr1  6000 12000  6001      - HAVANA transcript    NA    NA   GeneB
#> 6     chr1  6000  6500   501      - HAVANA       exon    NA    NA   GeneB
#>       gene_name transcript_id exon_number
#> 1 UnsplicedGene          <NA>        <NA>
#> 2          <NA>     GeneA-001        <NA>
#> 3          <NA>     GeneA-001           1
#> 4   SplicedGene          <NA>        <NA>
#> 5          <NA>     GeneB-001        <NA>
#> 6          <NA>     GeneB-001           1