## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval = FALSE------------------------------------------------------------- # # install.packages("BiocManager") # BiocManager::install("fobitools") ## ----warning = FALSE, message = FALSE, comment = FALSE------------------------ library(fobitools) ## ----warning = FALSE, message = FALSE, comment = FALSE------------------------ library(dplyr) library(kableExtra) ## ----warning = FALSE, message = FALSE, comment = FALSE------------------------ # select 300 random metabolites from FOBI idx_universe <- sample(nrow(fobitools::idmap), 300, replace = FALSE) metaboliteUniverse <- fobitools::idmap %>% dplyr::slice(idx_universe) %>% pull(FOBI) # select 10 random metabolites from metaboliteUniverse that are associated with 'Red meat' (FOBI:0193), # 'Lean meat' (FOBI:0185) , 'egg food product' (FOODON:00001274), # or 'grape (whole, raw)' (FOODON:03301702) fobi_subset <- fobitools::fobi %>% # equivalent to `parse_fobi()` filter(FOBI %in% metaboliteUniverse) %>% filter(id_BiomarkerOf %in% c("FOBI:0193", "FOBI:0185", "FOODON:00001274", "FOODON:03301702")) %>% dplyr::slice(sample(nrow(.), 10, replace = FALSE)) metaboliteList <- fobi_subset %>% pull(FOBI) ## ----warning = FALSE, eval = FALSE-------------------------------------------- # fobitools::ora(metaboliteList = metaboliteList, # metaboliteUniverse = metaboliteUniverse, # subOntology = "food", # pvalCutoff = 0.01) ## ----warning = FALSE, message = FALSE, comment = FALSE, echo = FALSE---------- res_ora <- fobitools::ora(metaboliteList = metaboliteList, metaboliteUniverse = metaboliteUniverse, subOntology = "food", pvalCutoff = 0.01) ## ----warning = FALSE, message = FALSE, comment = FALSE, echo = FALSE---------- kbl(res_ora, row.names = FALSE, booktabs = TRUE) %>% kable_styling(latex_options = c("striped")) ## ----warning = FALSE, message = FALSE, comment = FALSE, fig.align = "center", fig.height = 8, fig.width = 10---- terms <- fobi_subset %>% pull(id_code) # create the associated graph fobitools::fobi_graph(terms = terms, get = "anc", labels = TRUE, legend = TRUE) ## ----------------------------------------------------------------------------- sessionInfo()