In montilab/iEDGE: integrative analysis of (epi-)DNA and gene expression data

In this tutorial, we run iEDGE on the TCGA PAAD dataset. To achieve reasonable run time, we restrict the run to the first 3 copy number alterations in the dataset.

iEDGE execution

For this tutorial, we use a processed iEDGE object. See iEDGE analysis of a simulated dataset for a description of the object's components. Also, see scripts_TCGA_pancancer/1.preprocess_all_TCGA.R in the vignette folder for an illustration of how to datasets were preprocessed for the TCGA pancancer analysis.

f_in <- "./tcga_sample_data/TCGA_PAAD.RDS"
header <- paste(gsub(".RDS", "", basename(f_in)), sep = "")
cat(paste("header: ", header, "\n", sep = ""))

dat <- readRDS(f_in)

# subset dat to first 3 copy number alterations
names(dat)
cn <- dat$cn[1:3,]
gep <- dat$gep
cisgenes <- dat$cisgenes[1:3]

dat <- list(cn = cn, gep = gep, cisgenes = cisgenes)

# read in geneset annotation files for pathway enrichment analysis
gs.dir <- "./tcga_sample_data"
gs.names <- c("h.all.v5.0.symbols.gmt","c2.cp.v5.0.symbols.gmt", "c3.tft.v5.0.symbols.gmt")
gs.names <- paste(gs.dir, gs.names, sep = "/")

# directory for output reports
f_out <- "."

res <- run_iEDGE(dat, header, f_out, 
                 gs.file = gs.names, 
                 gepid = "gene_symbol",
                 cnid = "Unique.Name", 
                 cndir = "alteration_direction",
                 fdr.cis.cutoff = 0.25, 
                 fdr.trans.cutoff = 0.01,
                 fc.cis = 1.2,
                 fc.trans = 1.5,
                 min.drawsize = 3,
                 onesided.cis = TRUE, 
                 onesided.trans = FALSE,
                 uptest = "Amplification",
                 downtest = "Deletion", 
                 min.group = 2,
                 prune.col = "fdr",
                 prune.thres = 0.05,
                 hyperthres = 0.25,
                 cis.boxplot = TRUE,
                 trans.boxplot = FALSE,
                 bipartite = TRUE,
                 enrichment = TRUE,
                 html = TRUE)