Read a GFF/GTF/GVT file

This is a lightweight wrapper to the import family of functions defined in rtracklayer.

read_gff(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)

read_gff1(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)

read_gff2(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)

read_gff3(file, col_names = NULL, genome_info = NULL, overlap_ranges = NULL)

Arguments

file

A path to a file or a connection.

col_names

An optional character vector for parsing specific columns in file that are part of the GFF specification. These should name either fixed fields, like source or type, or, for GFF2 and GFF3, any attribute.

genome_info

An optional character string or a Ranges object that contains information about the genome build. For example the UCSC identifier "hg19" will add build information to the returned GRanges.

overlap_ranges

An optional Ranges object. Only the intervals in the file that overlap the Ranges will be returned.

Value

A GRanges object

a GRanges object

See also

rtracklayer::GFFFile()

Examples

test_path <- system.file("tests", package = "rtracklayer")
# gff3
test_gff3 <- file.path(test_path, "genes.gff3")
gr <- read_gff3(test_gff3)
gr
#> GRanges object with 31 ranges and 10 metadata columns:
#>        seqnames      ranges strand |      source     type     score     phase
#>           <Rle>   <IRanges>  <Rle> |    <factor> <factor> <numeric> <integer>
#>    [1]    chr10 92828-95504      - | rtracklayer     gene         5      <NA>
#>    [2]    chr10 92828-95178      - | rtracklayer     mRNA        NA      <NA>
#>    [3]    chr10 92828-95504      - | rtracklayer     mRNA        NA      <NA>
#>    [4]    chr10 92828-94054      - | rtracklayer     exon        NA      <NA>
#>    [5]    chr10 92997-94054      - | rtracklayer     CDS         NA      <NA>
#>    ...      ...         ...    ... .         ...      ...       ...       ...
#>   [27]    chr12 89675-89827      + | rtracklayer     CDS         NA      <NA>
#>   [28]    chr12 90587-90655      + | rtracklayer     exon        NA      <NA>
#>   [29]    chr12 90587-90655      + | rtracklayer     CDS         NA      <NA>
#>   [30]    chr12 90796-91263      + | rtracklayer     exon        NA      <NA>
#>   [31]    chr12 90796-91263      * | rtracklayer     CDS         NA      <NA>
#>                   ID        Name        geneName           Alias      genome
#>          <character> <character>     <character> <CharacterList> <character>
#>    [1] GeneID:347688       TUBB8 tubulin, beta 8  FLJ40100,TUBB8        hg19
#>    [2]           873       TUBB8            <NA>                        <NA>
#>    [3]           872       TUBB8            <NA>                        <NA>
#>    [4]          <NA>        <NA>            <NA>                        <NA>
#>    [5]          <NA>        <NA>            <NA>                        <NA>
#>    ...           ...         ...             ...             ...         ...
#>   [27]          <NA>        <NA>            <NA>                        <NA>
#>   [28]          <NA>        <NA>            <NA>                        <NA>
#>   [29]          <NA>        <NA>            <NA>                        <NA>
#>   [30]          <NA>        <NA>            <NA>                        <NA>
#>   [31]          <NA>        <NA>            <NA>                        <NA>
#>                 Parent
#>        <CharacterList>
#>    [1]                
#>    [2]   GeneID:347688
#>    [3]   GeneID:347688
#>    [4]         872,873
#>    [5]         872,873
#>    ...             ...
#>   [27]            4644
#>   [28]            4644
#>   [29]            4644
#>   [30]            4644
#>   [31]            4644
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
# alternatively with read_gff
gr <- read_gff(test_gff3, genome_info = "hg19")
gr
#> GRanges object with 31 ranges and 10 metadata columns:
#>        seqnames      ranges strand |      source     type     score     phase
#>           <Rle>   <IRanges>  <Rle> |    <factor> <factor> <numeric> <integer>
#>    [1]    chr10 92828-95504      - | rtracklayer     gene         5      <NA>
#>    [2]    chr10 92828-95178      - | rtracklayer     mRNA        NA      <NA>
#>    [3]    chr10 92828-95504      - | rtracklayer     mRNA        NA      <NA>
#>    [4]    chr10 92828-94054      - | rtracklayer     exon        NA      <NA>
#>    [5]    chr10 92997-94054      - | rtracklayer     CDS         NA      <NA>
#>    ...      ...         ...    ... .         ...      ...       ...       ...
#>   [27]    chr12 89675-89827      + | rtracklayer     CDS         NA      <NA>
#>   [28]    chr12 90587-90655      + | rtracklayer     exon        NA      <NA>
#>   [29]    chr12 90587-90655      + | rtracklayer     CDS         NA      <NA>
#>   [30]    chr12 90796-91263      + | rtracklayer     exon        NA      <NA>
#>   [31]    chr12 90796-91263      * | rtracklayer     CDS         NA      <NA>
#>                   ID        Name        geneName           Alias      genome
#>          <character> <character>     <character> <CharacterList> <character>
#>    [1] GeneID:347688       TUBB8 tubulin, beta 8  FLJ40100,TUBB8        hg19
#>    [2]           873       TUBB8            <NA>                        <NA>
#>    [3]           872       TUBB8            <NA>                        <NA>
#>    [4]          <NA>        <NA>            <NA>                        <NA>
#>    [5]          <NA>        <NA>            <NA>                        <NA>
#>    ...           ...         ...             ...             ...         ...
#>   [27]          <NA>        <NA>            <NA>                        <NA>
#>   [28]          <NA>        <NA>            <NA>                        <NA>
#>   [29]          <NA>        <NA>            <NA>                        <NA>
#>   [30]          <NA>        <NA>            <NA>                        <NA>
#>   [31]          <NA>        <NA>            <NA>                        <NA>
#>                 Parent
#>        <CharacterList>
#>    [1]                
#>    [2]   GeneID:347688
#>    [3]   GeneID:347688
#>    [4]         872,873
#>    [5]         872,873
#>    ...             ...
#>   [27]            4644
#>   [28]            4644
#>   [29]            4644
#>   [30]            4644
#>   [31]            4644
#>   -------
#>   seqinfo: 298 sequences (2 circular) from hg19 genome