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knitr::purl("sample_workflow.Rmd", "sample_workflow.R")
library(magrittr) library(RMySQL) library(dplyr) library(stringr) library(edgeR) library(sitt) T0 <- "None" T1 <- "Pioglitazone" T2 <- "Metformin" T12 <- "Pioglitazone / Metformin" # enumerate theoretical outcome vectors th_vectors <- outcomeVectorsByMode() # connect to database CON <- dbConnect(MySQL(),...) # metadata -------------------------------------------------------------------- combo_exists <- sitt::isValidCombination(T1, T2, DRUG_COMBINATION = TRUE) metadata <- getInteraction(CON, T1, T2, T12, "EC") %>% sitt::filterMetadata(conc = "Mid", sex = "M", cell.type = "EC") metadata <- getVehicles(CON, "EC", metadata) counts <- getExpectedCounts(CON, metadata, level = "gene") genes <- getGeneMetadata(CON, counts, level = "gene") counts <- asCountsMatrix(counts) interaction <- edgeRModeClassifier(counts, genes, metadata, DRUG_COMBINATION = TRUE, alpha = 0.05) go_data <- getGOTermsForAllModes(interaction$voom, interaction$interaction.tbl)
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