In CBIIT/rcellminerElasticNet: rcellminerElasticNet

require("knitr")
opts_knit$set(root.dir="..")
opts_chunk$set(fig.align="center", fig.width=6, fig.height=6, dpi=300)

Purpose

• Make summary figure of Elastic Net results for the NCI-60 SWATH data

Set Up

library(stringr)
library(rcellminer)

# Parameters are set at top in YAML section
commonFlag <- params$commonFlag
dataDir <- params$dataDir
outputDir <- params$outputDir

commonFlag
dataDir
outputDir

#DEBUG 
#commonFlag <- TRUE

enDataDir <- file.path(dataDir, allDataDir)
outputDir <- outputDir
outFile <- "en_annot_table.txt"

if(commonFlag) {
  enDataDir <- file.path(dataDir, commonDataDir)
  outFile <- paste0("common_", outFile)  
}

enResultFiles <- dir(enDataDir, pattern = ".Rdata", full.names=TRUE)
enResultFiles <- enResultFiles[!str_detect(enResultFiles, pattern = "invalid")]

molDB <- rcellminer::getAllFeatureData(rcellminerData::molData)

nci60Act <- exprs(getAct(rcellminerData::drugData))

Construct Table

enResultToPreds <- setNames(vector(mode = "list", length = length(enResultFiles)),
                            enResultFiles)

i <- 0
for (enFilePath in names(enResultToPreds)){
  i <- i + 1
  tmpEnv <- new.env()
  load(enFilePath, envir = tmpEnv)
  enResultToPreds[[enFilePath]] <- names(tmpEnv$elNetResults$predictorWts)
  cat(i, sep = "\n")
}

numDrugPredPairs <- length(c(enResultToPreds, recursive = TRUE))

predAnnotTab <- data.frame(nsc = character(numDrugPredPairs),
                           drugName = NA, moa = NA, respCor = NA, dataType = NA, 
                           gene = NA, nodeType = NA, cancerConsistency = NA, pmid = NA,
                           notes = NA, stringsAsFactors = FALSE)

i <- 0
for (enFilePath in names(enResultToPreds)){
  tmp <- str_split(enFilePath, pattern = ".Rdata")[[1]][1]
  nsc <- str_split(tmp, pattern = "_NSC_")[[1]][2]
  if (!is.null(enResultToPreds[[enFilePath]])){
    for (predName in enResultToPreds[[enFilePath]]){
      i <- i + 1
      predAnnotTab[i, "nsc"] <- nsc
      predAnnotTab[i, "dataType"] <- rcellminer::getMolDataType(predName)
      predAnnotTab[i, "gene"] <- rcellminer::removeMolDataType(predName)
      cat(i, sep = "\n")
    }
  }
}

predAnnotTab <- base::unique(predAnnotTab)

for (i in seq_len(nrow(predAnnotTab))){
  nsc <- predAnnotTab[i, "nsc"]
  dataType <- predAnnotTab[i, "dataType"]
  gene <- predAnnotTab[i, "gene"]

  predAnnotTab[i, "drugName"] <- rcellminer::getDrugName(nsc)
  predAnnotTab[i, "moa"] <- paste0(rcellminer::getDrugMoaList(nsc), collapse = "|")
  predAnnotTab[i, "respCor"] <- cor.test(
    x = nci60Act[nsc, , drop = TRUE],
    y = molDB[[dataType]][gene, , drop = TRUE]
  )$estimate

  cat(i, sep = "\n")
}

write.table(predAnnotTab, file=file.path(outputDir, outFile), 
            quote=FALSE, sep="\t", row.names=FALSE, col.names=TRUE, na="")

Session Info

sessionInfo()

CBIIT/rcellminerElasticNet documentation built on Sept. 8, 2020, 6:21 p.m.