vignettes/sample_workflow.md

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

Sample Workflow for Sitagliptin / Metformin

To generate an R script with this code:

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(), user = "eld", password = '5thStreet',
                 dbname = 'eld_v4')

# 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)

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