Merge pull request hyginn#21 from wonjunetai/master

importFilterHypermutators function

NAMESPACE

@@ -10,6 +10,7 @@ export(fastMapUpdate)
 export(findUUID)
 export(getProvenance)
 export(getUUID)
+export(importFilterHypermutators)
 export(importM.COSMIC)
 export(importNet.STRING)
 export(isHGNCsymbol)

R/importFilterHypermutators.R

@@ -0,0 +1,225 @@
+# importFilterHypermutators.R
+
+#' Filters out hypermutators
+#'
+#' \code{importFilterHypermutators} identifies the number of SNV and CNA
+#' mutations for each sample and removes the samples from rSNV and rCNA
+#' datasets. Default threshold for removal is 400 mutations per sample.
+#'
+#' @param rSNVFileIn A vector of local file names of rSNV
+#' @param rCNAFileIn A vector of local file names of rCNA
+#' @param dOut Directory to store output, defaults to getwd().
+#' @param xS Mutation threshold. 400 by default.
+#' @param silent Controls whether output to console should be suppressed. FALSE
+#'   by default.
+#' @param writeLog Controls whether writing the result to the global logfile is
+#'   enabled. TRUE by default.
+#' @param writeDetailedLog Flag for extra details about log. TRUE by default.
+#'
+#' @examples
+#' \dontrun{
+#'     importFilterHypermutators(rSNVFileIn, rCNAFileIn, dOut, xS)
+#' }
+#'
+#' @export
+importFilterHypermutators <- function(rSNVFileIn = c(),
+                                      rCNAFileIn = c(),
+                                      dOut = getwd(),
+                                      xS = 400,
+                                      silent = FALSE,
+                                      writeLog = TRUE,
+                                      writeDetailedLog = TRUE) {
+
+    ## VALIDATE PARAMS ########
+    # make sure that files actually exist
+    for (file in rSNVFileIn) {
+        r <- .checkArgs(file, like = "FILE_E", checkSize = TRUE)
+        if (length(r) > 0) {
+            stop(r)
+        }
+    }
+
+    for (file in rCNAFileIn) {
+        r <- .checkArgs(file, like = "FILE_E", checkSize = TRUE)
+        if (length(r) > 0) {
+            stop(r)
+        }
+    }
+
+    # make sure that output directory is valid
+    r <- .checkArgs(dOut, like = "DIR", checkSize = TRUE)
+    if(length(r) > 0) {
+        stop(r)
+    }
+
+    r <- c(r, .checkArgs(xS, like = 1, checkSize = TRUE))
+    if (length(r) > 0) {
+        stop(r)
+    }
+
+    # set up hashes
+    hashTable <- new.env(hash = TRUE)
+    totalSamples <- 0
+
+    ## COUNT MUTATIONS ########
+    # for each file in rCNAFileIn
+    for (file in rCNAFileIn) {
+        # readRDS, count gene CNAs and add to hash for sample @ CNA and nMUT
+        rCNA <- readRDS(file)
+        for (sample in colnames(rCNA)[4:length(colnames(rCNA))]) {
+            totalSamples <- totalSamples + 1
+            # if key is in hash, increment CNA and nMUT for every gene if there is an abberation
+            for (copyNumberValue in rCNA[[sample]]) {
+                copyNumberValue <- as.double(copyNumberValue)
+                if (copyNumberValue != 0) {
+                    if (!is.null(hashTable[[sample]])) {
+                        prevCNACount <- hashTable[[sample]]$CNA
+                        prevTotalCount <- hashTable[[sample]]$total
+                        assign(sample, list(CNA = prevCNACount + 1, SNV = 0, total = prevTotalCount + 1), envir = hashTable)
+                    } else {
+                        assign(sample, list(CNA = 1, SNV = 0, total = 1), envir = hashTable)
+                    }
+                }
+            }
+        }
+    }
+
+    # for each file in rSNVFileIn
+    for (file in rSNVFileIn) {
+        # readRDS, increment counter for SNV and nMUT
+        rSNV <- readRDS(file)
+        for (i in 1:length(rSNV$Tumor_Sample_Barcode)) {
+            # need to substitute dashes with period for consistency in files
+            sample <-  gsub("-", ".", rSNV$Tumor_Sample_Barcode[i])
+            totalSamples <- totalSamples + 1
+
+            # Present a progress bar.
+            if (!silent) {
+                .pBar(i, length(rSNV$Tumor_Sample_Barcode))
+            }
+
+            # if key is in hash, increment SNV and nMUT
+            if (!is.null(hashTable[[sample]])) {
+                prevCNACount <- hashTable[[sample]]$CNA
+                prevSNVCount <- hashTable[[sample]]$SNV
+                prevTotalCount <- hashTable[[sample]]$total
+                assign(sample, list(CNA = prevCNACount, SNV = prevSNVCount + 1, total = prevTotalCount + 1), envir = hashTable)
+            } else {
+                assign(sample, list(CNA = 0, SNV = 1, total = 1), envir = hashTable)
+            }
+        }
+    }
+
+    ## ASSESS MUTATIONS AND LOG STATISTICS #######
+
+    # log global statistics:
+    numSamplesBothSNVAndCNA <- 0
+    numSamplesOnlyCNA <- 0
+    numSamplesOnlySNV <- 0
+    numSamplesNoChange <- 0
+    numSamplesExceedThresh <- 0
+    numRemovedSamples <- 0
+    removedSamples <- c()
+
+    for (sample in ls(hashTable)) {
+        # num samples with only CNA
+        if (hashTable[[sample]]$SNV == 0 && hashTable[[sample]]$CNA > 0) {
+            numSamplesOnlyCNA <- numSamplesOnlyCNA + 1
+        }
+        # num samples with only SNV
+        if (hashTable[[sample]]$CNA == 0 && hashTable[[sample]]$SNV > 0) {
+            numSamplesOnlySNV <- numSamplesOnlySNV + 1
+        }
+        # num samples with both SNV and CNA
+        if (hashTable[[sample]]$CNA > 0 && hashTable[[sample]]$SNV > 0) {
+            numSamplesBothSNVAndCNA <- numSamplesBothSNVAndCNA + 1
+        }
+        # num samples that exceeded threshold and need to be removed
+        if (hashTable[[sample]]$total > xS) {
+            numRemovedSamples <- numRemovedSamples + 1
+            removedSamples <- c(removedSamples, sample)
+        }
+        # num samples with no change
+        if (hashTable[[sample]]$total <= xS) {
+            numSamplesNoChange <- numSamplesNoChange + 1
+        }
+    }
+
+    ## PROCESS FILES AND UPDATE METADATA ##########
+
+    # for each rCNAFileIn
+    for (file in rCNAFileIn) {
+        rCNA <- readRDS(file)
+
+        # remove sample if sample in `removedSamples`
+        newRCNA <- rCNA[, !(names(rCNA) %in% removedSamples)]
+
+        # update metadata
+        getUUID("newRCNA", overwrite = TRUE)
+        # ToDo: record updated UUID in log-file
+        # ToDo: test that UUID is _actually_ being updated.
+
+
+        # save new CNAFile with "filtered" prepended to filename
+        saveRDS(newRCNA, file = paste(dOut, "/filteredHypermutators_", basename(file), sep = ""))
+    }
+
+    # for each rSNVFileIn
+    for (file in rSNVFileIn) {
+        rSNV <- readRDS(file)
+
+        # for each sample (need to gsub("-", ".", sample)), if sample in `removedSamples` remove it
+        newRSNV <- rSNV[, !(gsub("-", ".", rSNV$Tumor_Sample_Barcode) %in% removedSamples)]
+
+        # update metadata
+        getUUID("newRSNV", overwrite = TRUE)
+        # ToDo: record updated UUID in log-file
+        # ToDo: test that UUID is _actually_ being updated.
+
+        # save new SNVFile
+        saveRDS(newRSNV, file = paste(dOut, "/filteredHypermutators_", basename(file), sep = ""))
+    }
+
+    ## LOGGING ###############
+
+    if(writeLog) {
+
+        logTitle <- "importFilterHypermutators"
+
+        # Compile function call record
+        logCall <- character()
+        logCall[1] <- "importFilterHypermutators("
+        logCall[2] <- sprintf("rSNVFileIn = (%s)", paste(rSNVFileIn, collapse(", ")))
+        logCall[3] <- sprintf("rCNAFileIn = (%s)", paste(rCNAFileIn, collapse(", ")))
+        logCall[4] <- sprintf("dOut = \"%s\", ", dOut)
+        logCall[5] <- sprintf("xS = \"%s\", ", as.character(xS))
+        logCall[6] <- sprintf("silent = %s, ", as.character(silent))
+        logCall[7] <- sprintf("writeLog = %s)", as.character(writeLog))
+        logCall <- paste0(logCall, collapse = "")
+
+        # Record progress information
+        logNotes <- character()
+        logNotes <- c(logNotes, sprintf("Removed %s of %s samples", numRemovedSamples, totalSamples))
+
+        if (writeDetailedLog) {
+            logNotes <- c(logNotes, sprintf("%s of samples had both SNV and CNA", numSamplesBothSNVAndCNA/totalSamples))
+            logNotes <- c(logNotes, sprintf("%s of samples had only CNA", numSamplesOnlyCNA/totalSamples))
+            logNotes <- c(logNotes, sprintf("%s of samples had only SNV", numSamplesOnlySNV/totalSamples))
+            logNotes <- c(logNotes, sprintf("%s of samples had no change", numSamplesNoChange/totalSamples))
+            logNotes <- c(logNotes, sprintf("%s of samples exceeded threshold of %s", numSamplesExceedThresh/totalSamples, xS))
+
+            # Accumulate all removed samples
+            for (sample in removedSamples) {
+                logNotes <- c(logNotes, sprintf("%s was removed", sample))
+            }
+        }
+
+        # # send info to log file
+        logEvent(eventTitle = logTitle,
+                 eventCall = logCall,
+                 notes = logNotes)
+    }
+
+}
+
+# [END]

tests/testthat/testFilter.R

@@ -0,0 +1,108 @@
+# testFilter
+#
+#
+context("Tests for importFilterHypermutators.R")
+
+# ==== BEGIN SETUP AND PREPARE =================================================
+OLOG <- as.character(getOption("rete.logfile"))   # save original logfile name
+logFileName(fPath = tempdir(), setOption = TRUE)  # make tempdir() the log dir
+logName <- unlist(getOption("rete.logfile"))
+if (file.exists(logName)) { file.remove(logName)}
+
+SNVfileName <- 'devSNV.rds'
+CNAfileName <- 'devCNA.rds'
+
+filteredSNVfileName <- paste(getwd(), "/filteredHypermutators_", basename(SNVfileName), sep = "")
+filteredCNAfileName <- paste(getwd(), "/filteredHypermutators_", basename(CNAfileName), sep = "")
+# ==== END SETUP AND PREPARE ===================================================
+
+
+# ==== importFilterHypermutators() =============================================
+
+# set up a tempdir and tempfiles for outputs of importFilterHypermutators
+test_that("importFilterHypermutators works correctly on valid input", {
+    # run importFilterHypermutators on valid input
+    expect_error(importFilterHypermutators(rSNVFileIn = c(SNVfileName),
+                                           rCNAFileIn = c(CNAfileName),
+                                           dOut = getwd(),
+                                           xS = 400,
+                                           silent = FALSE,
+                                           writeLog = TRUE), NA)
+
+    if (file.exists(filteredSNVfileName)) { file.remove(filteredSNVfileName)}
+    if (file.exists(filteredCNAfileName)) { file.remove(filteredCNAfileName)}
+})
+
+test_that("importFilterHypermutators rejects invalid dOut arguments", {
+    # check for NULL object
+    expect_error(importFilterHypermutators(rSNVFileIn = c(SNVfileName),
+                                           rCNAFileIn = c(CNAfileName),
+                                           dOut = NULL,
+                                           xS = 400,
+                                           silent = FALSE,
+                                           writeLog = TRUE))
+    # check for paths that don't exist
+    expect_error(importFilterHypermutators(rSNVFileIn = c(SNVfileName),
+                                           rCNAFileIn = c(CNAfileName),
+                                           dOut = 'no/such/path',
+                                           xS = 400,
+                                           silent = FALSE,
+                                           writeLog = TRUE))
+})
+
+test_that("importFilterHypermutators rejects invalid xS arguments", {
+    # check for including NULL objects
+    expect_error(importFilterHypermutators(rSNVFileIn = c(SNVfileName),
+                                           rCNAFileIn = c(CNAfileName),
+                                           xS = NULL,
+                                           silent = FALSE,
+                                           writeLog = TRUE))
+    # check character
+    expect_error(importFilterHypermutators(rSNVFileIn = c(SNVfileName),
+                                           rCNAFileIn = c(CNAfileName),
+                                           xS = "400",
+                                           silent = FALSE,
+                                           writeLog = TRUE))
+})
+
+test_that("importFilterHypermutators correctly removes hypermutators", {
+    # run importFilterHypermutators with a single hypermutator
+    testCNA <- readRDS(CNAfileName)
+    testSNV <- readRDS(SNVfileName)
+
+    # start off with a known number of samples in each CNA and SNV file
+    expect_equal(length(colnames(testCNA)[4:length(colnames(testCNA))]), 579)
+    expect_equal(length(testSNV$Tumor_Sample_Barcode), 15)
+
+    expect_error(importFilterHypermutators(rSNVFileIn = c(SNVfileName),
+                                           rCNAFileIn = c(CNAfileName),
+                                           xS = 15,
+                                           silent = FALSE,
+                                           writeLog = TRUE), NA)
+
+    # check output file
+    processedCNA <- readRDS(filteredCNAfileName)
+    processedSNV <- readRDS(filteredSNVfileName)
+
+    # expect that 458 samples are removed from rCNA (579 - 458 = 121)
+    expect_equal(length(colnames(processedCNA)[4:length(colnames(processedCNA))]), 121)
+
+    # expect that no samples are removed from rSNV
+    expect_equal(length(processedSNV$Tumor_Sample_Barcode), 15)
+
+    # test cleanup
+    if (file.exists(filteredSNVfileName)) { file.remove(filteredSNVfileName)}
+    if (file.exists(filteredCNAfileName)) { file.remove(filteredCNAfileName)}
+})
+
+# ==== BEGIN TEARDOWN AND RESTORE ==============================================
+logName <- unlist(getOption("rete.logfile"))
+if (file.exists(logName)) { file.remove(logName)}
+options("rete.logfile" = OLOG)
+
+# another check for function artifacts
+if (file.exists(filteredSNVfileName)) { file.remove(filteredSNVfileName)}
+if (file.exists(filteredCNAfileName)) { file.remove(filteredCNAfileName)}
+# ==== END  TEARDOWN AND RESTORE ===============================================
+
+# [END]