Supports organism detection from Ensembl identifier or genome build.
Only the first match is returned. We're using a while loop approach here so we can skip transgenes or spike-ins. The function fails after a maximum of 50 unknowns, for speed.
Full latin organism name. Stops on match failure.
Caenorhabditis elegans (roundworm)
Danio rerio (zebrafish)
Drosophila melanogaster (fruitfly)
Gallus gallus (chicken)
Homo sapiens (human)
Mus musculus (mouse)
Ovis aries (sheep)
Rattus norvegicus (rat)
Saccharomyces cerevisiae (yeast)
character method conflicts with annotate
package, which gets loaded into the namespace when DESeq2 is attached.
Instead, we're exporting the character method here as a separate function
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## Match by gene identifier. detectOrganism("ENSG00000000003") ## Match by genome build. detectOrganism("GRCh38") # Ensembl detectOrganism("hg38") # UCSC ## Match by alternate organism name. detectOrganism("H. sapiens") detectOrganism("hsapiens") ## The function will skip transgenes/spike-ins until we find a match. detectOrganism(c("EGFP", "TDTOMATO", "ENSG00000000003")) ## But it only returns the first match, if there are multiple genomes. detectOrganism(c("ENSG00000000003", "ENSMUSG00000000001"))
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