## ---- eval=FALSE-------------------------------------------------------------- # 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") ## ----setup-------------------------------------------------------------------- library(orthogene) data("exp_mouse") # Setting to "homologene" for the purposes of quick demonstration. # We generally recommend using method="gprofiler" (default). method <- "homologene" ## ----------------------------------------------------------------------------- matches <- orthogene::infer_species(gene_df = exp_mouse, method = method) ## ----------------------------------------------------------------------------- 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) ## ----------------------------------------------------------------------------- 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) ## ----------------------------------------------------------------------------- matches <- orthogene::infer_species(gene_df = exp_human, test_species = method, method = method) ## ----Session Info------------------------------------------------------------- utils::sessionInfo()