## ----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(version = "3.14") # # 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" ## ----convert_orthologs-------------------------------------------------------- gene_df <- orthogene::convert_orthologs(gene_df = exp_mouse, gene_input = "rownames", gene_output = "rownames", input_species = "mouse", output_species = "human", non121_strategy = "drop_both_species", method = method) knitr::kable(as.matrix(head(gene_df))) ## ----map_species-------------------------------------------------------------- species <- orthogene::map_species(species = c("human",9544,"mus musculus", "fruit fly","Celegans"), output_format = "scientific_name") print(species) ## ----report_orthologs--------------------------------------------------------- orth_zeb <- orthogene::report_orthologs(target_species = "zebrafish", reference_species = "human", method_all_genes = method, method_convert_orthologs = method) knitr::kable(head(orth_zeb$map)) knitr::kable(orth_zeb$report) ## ----map_genes---------------------------------------------------------------- genes <- c("Klf4", "Sox2", "TSPAN12","NM_173007","Q8BKT6",9999, "ENSMUSG00000012396","ENSMUSG00000074637") mapped_genes <- orthogene::map_genes(genes = genes, species = "mouse", drop_na = FALSE) knitr::kable(head(mapped_genes)) ## ----------------------------------------------------------------------------- data("exp_mouse_enst") knitr::kable(tail(as.matrix(exp_mouse_enst))) exp_agg <- orthogene::aggregate_mapped_genes(gene_df=exp_mouse_enst, input_species="mouse", agg_fun = "sum") knitr::kable(tail(as.matrix(exp_agg))) ## ----all_genes---------------------------------------------------------------- genome_mouse <- orthogene::all_genes(species = "mouse", method = method) knitr::kable(head(genome_mouse)) ## ----Session Info------------------------------------------------------------- utils::sessionInfo()