alcoholic gemma

ethanol.R

devtools::load_all()
library(magrittr)
datasets <- get_datasets(uris = 'http://purl.obolibrary.org/obo/MONDO_0000408')
relevant_terms <- attributes(datasets)$filter %>% stringr::str_extract_all('http.*?(?=,|\\))') %>% {.[[1]]}

relevant_terms %<>% c('http://purl.obolibrary.org/obo/CHEBI_16236')


dataset_contrasts <- datasets$experiment.shortName %>% 
    lapply(function(x){
        out = get_dataset_differential_expression_analyses(x)
    }) %>% do.call(rbind,.)


relevant_contrasts <- dataset_contrasts %>% dplyr::filter(sapply(experimental.factors,function(x){
    any(x$value.URI %in% relevant_terms | x$object.URI %in% relevant_terms)
}))

differentials <- relevant_contrasts$result.ID %>% lapply(function(x){
    get_differential_expression_values(resultSet = x)[[1]]
})



condition_diffs <- seq_along(differentials) %>% lapply(function(i){
    # iterate over the differentials
    diff = differentials[[i]]
    # get the contrast information about the differential
    contrast = relevant_contrasts[i,]
    p_vals = diff[[paste0('contrast_',contrast$contrast.ID,"_pvalue")]]
    log2fc = diff[[paste0('contrast_',contrast$contrast.ID,"_log2fc")]]
    genes = diff$GeneSymbol
    
    data.frame(genes,p_vals,log2fc)
})

names(condition_diffs) = paste0(relevant_contrasts$experiment.ID,'.',
                                relevant_contrasts$result.ID,'.',
                                relevant_contrasts$contrast.ID)

condition_diffs %<>% lapply(function(x){
    x$p_adj <- x$p_vals %>% p.adjust('fdr')
    return(x)
})