if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") # orthogene is only available on Bioconductor>=3.14 if(BiocManager::version()<"3.14") BiocManager::install(update = TRUE, ask = FALSE) BiocManager::install("orthogene")
library(orthogene) data("exp_mouse") # Setting to "homologene" for the purposes of quick demonstration. # We generally recommend using method="gprofiler" (default). method <- "homologene"
It's not always clear whether a dataset is using the original species gene names, human gene names, or some other species' gene names.
infer_species
takes a list/matrix/data.frame with genes and
infers the species that they best match to!
For the sake of speed, the genes extracted from gene_df
are tested against genomes from only the following 6 test_species
by default:
- human
- monkey
- rat
- mouse
- zebrafish
- fly
However, you can supply your own list of test_species
, which will
be automatically be mapped and standardised using map_species
.
matches <- orthogene::infer_species(gene_df = exp_mouse, method = method)
To create an example dataset, turn the gene names into rat genes.
exp_rat <- orthogene::convert_orthologs(gene_df = exp_mouse, input_species = "mouse", output_species = "rat", method = method)
matches <- orthogene::infer_species(gene_df = exp_rat, method = method)
To create an example dataset, turn the gene names into human genes.
exp_human <- orthogene::convert_orthologs(gene_df = exp_mouse, input_species = "mouse", output_species = "human", method = method)
matches <- orthogene::infer_species(gene_df = exp_human, method = method)
test_species
You can even supply test_species
with the name of one of the R packages that
orthogene
gets orthologs from. This will test against all species available
in that particular R package.
For example, by setting test_species="homologene"
we automatically test for
% gene matches in each of the 20+ species available in homologene
.
matches <- orthogene::infer_species(gene_df = exp_human, test_species = method, method = method)
utils::sessionInfo()
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