iEDGE analysis of the TCGA PAAD dataset

Amy Li

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)

iEDGE HTML report

The HTML report of this run is contained here