vignettes/sitagliptin_metformin_workflow.md

In taylo5jm/interactions: Classification of gene expression profile sets generated from combination stimuli

Sitagliptin + Metformin Example Workflow

# signal_interactions
lapply(dbListConnections(MySQL()), dbDisconnect)
library(magrittr)
library(RMySQL)
library(dplyr)
library(stringr)
library(edgeR)
library(sitt)
library(topGO)
set.seed(252)

T0 <- "None"
T1 <- "Sitagliptin"
T2 <- "Metformin"
T12 <- "Sitagliptin / Metformin"
cell_type <- "EC"
alpha <- 0.01

th_vectors <- outcomeVectorsByMode()
# connect to database
CON <- dbConnect(MySQL(), user = "eld", password = '5thStreet',
                 dbname = 'eld_v4')
# metadata --------------------------------------------------------------------
combo_exists <- isValidCombination(T1, T2,
                                   DRUG_COMBINATION = TRUE)
metadata <- getInteraction(CON, T1, T2,
                           T12, cell_type) %>%
  filterMetadata(conc = "Mid", sex = "M", cell.type = cell_type)
metadata <- getVehicles(CON, cell_type, metadata)
print(metadata)
# counts
counts <- sitt::getExpectedCounts(CON, metadata, level = "gene")


genes <- getGeneMetadata(CON, counts, level = "gene")
counts <- asCountsMatrix(counts)
interaction <- edgeRModeClassifier(counts, genes, metadata,
                                   DRUG_COMBINATION = TRUE,
                                   alpha = alpha)
counts <- counts[,sample(ncol(counts))]
interaction_null <- edgeRModeClassifier(counts, genes, metadata,
                                        DRUG_COMBINATION = TRUE,
                                        alpha = alpha)
go_data <- getGOTermsForAllModes(interaction$voom,
                                 interaction$interaction.tbl)
go_data_null <- getGOTermsForAllModes(interaction_null$voom,
                                      interaction_null$interaction.tbl)


interaction <- list(list(interaction = interaction,
                         go.data = go_data),
                    list(interaction = interaction_null,
                         go.data = go_data_null))
names(interaction) <- c("sample", "null")
this_path <- paste0("data/",
                   paste(T1, T2, cell_type, alpha, sep = "_"),
                   ".rda")
save(interaction, file = this_path)

taylo5jm/interactions documentation built on May 31, 2019, 3:57 a.m.