exampleZv9_annot {CAGEr} | R Documentation

## Example zebrafish annotation data

### Description

Annotation data for zebrafish's chromosome 17's interval 26000000-54000000 (Zv9/danRer7 genome), to be used in documentation examples.

### Usage

    exampleZv9_annot

### Format

An object of class `GRanges` of length 7467.

### Details

Data was retreived from ENSEMBL's Biomart server using a query to extract gene, transcripts and exon coordinates. For the record, here it is as URL (long, possibly overflowing).

http://mar2015.archive.ensembl.org/biomart/martview/78d86c1d6b4ef51568ba6d46f7d8b254?VIRTUALSCHEMANAME=default&ATTRIBUTES=drerio_gene_ensembl.default.structure.ensembl_gene_id|drerio_gene_ensembl.default.structure.ensembl_transcript_id|drerio_gene_ensembl.default.structure.start_position|drerio_gene_ensembl.default.structure.end_position|drerio_gene_ensembl.default.structure.transcript_start|drerio_gene_ensembl.default.structure.transcript_end|drerio_gene_ensembl.default.structure.strand|drerio_gene_ensembl.default.structure.chromosome_name|drerio_gene_ensembl.default.structure.external_gene_name|drerio_gene_ensembl.default.structure.gene_biotype|drerio_gene_ensembl.default.structure.exon_chrom_start|drerio_gene_ensembl.default.structure.exon_chrom_end|drerio_gene_ensembl.default.structure.is_constitutive|drerio_gene_ensembl.default.structure.rank&FILTERS=&VISIBLEPANEL=resultspanel

And here it is as XML.

    <?xml version="1.0" encoding="UTF-8"?>
    <!DOCTYPE Query>
    <Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
      <Dataset name = "drerio_gene_ensembl" interface = "default" >
        <Attribute name = "ensembl_gene_id" />
        <Attribute name = "ensembl_transcript_id" />
        <Attribute name = "start_position" />
        <Attribute name = "end_position" />
        <Attribute name = "transcript_start" />
        <Attribute name = "transcript_end" />
        <Attribute name = "strand" />
        <Attribute name = "chromosome_name" />
        <Attribute name = "external_gene_name" />
        <Attribute name = "gene_biotype" />
        <Attribute name = "exon_chrom_start" />
        <Attribute name = "exon_chrom_end" />
        <Attribute name = "is_constitutive" />
        <Attribute name = "rank" />
      </Dataset>
    </Query>

The downloaded file was then transformed as follows.

    x <- read.delim("~/Downloads/mart_export.txt", stringsAsFactors = FALSE)
    e <- GRanges(paste0("chr", x$Chromosome.Name), IRanges(x$Exon.Chr.Start..bp., x$Exon.Chr.End..bp.), ifelse(x$Strand + 1, "+", "-"))
    e$gene_name <- Rle(x$Associated.Gene.Name)
    e$transcript_type <- Rle(x$Gene.type)
    e$type <- "exon"
    e$type <- Rle(e$type)

    e <- GRanges(paste0("chr", x$Chromosome.Name), IRanges(x$Exon.Chr.Start..bp., x$Exon.Chr.End..bp.), ifelse(x$Strand + 1, "+", "-"))
    e$gene_name <- Rle(x$Associated.Gene.Name)
    e$transcript_type <- Rle(x$Gene.type)
    e$type <- "exon"
    e$type <- Rle(e$type)
    e <- sort(unique(e))

    g <- GRanges( paste0("chr", x$Chromosome.Name)
                , IRanges(x$Gene.Start..bp., x$Gene.End..bp.)
                , ifelse( x$Strand + 1, "+", "-"))

    g$gene_name <- Rle(x$Associated.Gene.Name)
    g$transcript_type <- Rle(x$Gene.type)
    g$type <- "gene"
    g$type <- Rle(g$type)
    g <- sort(unique(g))

    t <- GRanges( paste0("chr", x$Chromosome.Name)
                , IRanges(x$Transcript.Start..bp., x$Transcript.End..bp.)
                , ifelse( x$Strand + 1, "+", "-"))

    t$gene_name <- Rle(x$Associated.Gene.Name)
    t$transcript_type <- Rle(x$Gene.type)
    t$type <- "transcript"
    t$type <- Rle(t$type)
    t <- sort(unique(t))

    gff <- sort(c(g, t, e))
    gff <- gff[seqnames(gff) == "chr17"]
    gff <- gff[start(gff) > 26000000 & end(gff) < 54000000]
    seqlevels(gff) <- seqlevelsInUse(gff)

    save(gff, "data/exampleZv9_annot.RData", compress = "xz")

### Author(s)

Prepared by Charles Plessy plessy@riken.jp using archive ENSEMBL data.

### References

http://mar2015.archive.ensembl.org/biomart/

[Package CAGEr version 1.32.1 Index]