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elijah-tai · Mar 30, 2017 · dede433 · dede433
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commit dede433
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Showing 5 changed files with 41 additions and 18 deletions.
diff --git a/R/importFilterHypermutators.R b/R/importFilterHypermutators.R
@@ -66,10 +66,11 @@ importFilterHypermutators <- function(rSNVFileIn = c(),
     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)) {
+        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]]$CNA
@@ -102,7 +103,7 @@ importFilterHypermutators <- function(rSNVFileIn = c(),
                 prevCNACount <- hashTable[[sample]]$CNA
                 prevSNVCount <- hashTable[[sample]]$SNV
                 prevTotalCount <- hashTable[[sample]]$total
-                assign(sample, list(CNA = prevCNACount, SNV = prevSNVCount + 1, nMUT = prevTotalCount + 1), envir = hashTable)
+                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)
             }
@@ -122,24 +123,24 @@ importFilterHypermutators <- function(rSNVFileIn = c(),
 
     for (sample in ls(hashTable)) {
         # num samples with only CNA
-        if (hashTable[[sample]]$SNV == 0) {
+        if (hashTable[[sample]]$SNV == 0 && hashTable[[sample]]$CNA > 0) {
             numSamplesOnlyCNA <- numSamplesOnlyCNA + 1
         }
         # num samples with only SNV
-        else if (hashTable[[sample]]$CNA == 0) {
+        if (hashTable[[sample]]$CNA == 0 && hashTable[[sample]]$SNV > 0) {
             numSamplesOnlySNV <- numSamplesOnlySNV + 1
         }
         # num samples with both SNV and CNA
-        else if (hashTable[[sample]]$CNA > 0 && hashTable[[sample]]$SNV > 0) {
+        if (hashTable[[sample]]$CNA > 0 && hashTable[[sample]]$SNV > 0) {
             numSamplesBothSNVAndCNA <- numSamplesBothSNVAndCNA + 1
         }
-        # num samples that exceeded threshold and need removal
-        else if (hashTable[[sample]]$total > xS) {
+        # num samples that exceeded threshold and need to be removed
+        if (hashTable[[sample]]$total > xS) {
             numRemovedSamples <- numRemovedSamples + 1
             removedSamples <- c(removedSamples, sample)
         }
         # num samples with no change
-        else {
+        if (hashTable[[sample]]$total <= xS) {
             numSamplesNoChange <- numSamplesNoChange + 1
         }
     }
@@ -149,6 +150,7 @@ importFilterHypermutators <- function(rSNVFileIn = c(),
     # for each rCNAFileIn
     for (file in rCNAFileIn) {
         rCNA <- readRDS(file)
+
         # remove sample if sample in `removedSamples`
         newRCNA <- rCNA[, !(names(rCNA) %in% removedSamples)]
 

diff --git a/man/importFilterHypermutators.Rd b/man/importFilterHypermutators.Rd
diff --git a/inst/extdata/devCNA.rds → tests/testthat/devCNA.rds b/inst/extdata/devCNA.rds → tests/testthat/devCNA.rds
diff --git a/inst/extdata/devSNV.rds → tests/testthat/devSNV.rds b/inst/extdata/devSNV.rds → tests/testthat/devSNV.rds
diff --git a/tests/testthat/testFilter.R b/tests/testthat/testFilter.R
@@ -9,8 +9,8 @@ logFileName(fPath = tempdir(), setOption = TRUE)  # make tempdir() the log dir
 logName <- unlist(getOption("rete.logfile"))
 if (file.exists(logName)) { file.remove(logName)}
 
-SNVfileName <- '../../inst/extdata/devSNV.rds'
-CNAfileName <- '../../inst/extdata/devCNA.rds'
+SNVfileName <- 'devSNV.rds'
+CNAfileName <- 'devCNA.rds'
 
 filteredSNVfileName <- paste(getwd(), "/filteredHypermutators_", basename(SNVfileName), sep = "")
 filteredCNAfileName <- paste(getwd(), "/filteredHypermutators_", basename(CNAfileName), sep = "")
@@ -67,12 +67,28 @@ test_that("importFilterHypermutators rejects invalid xS arguments", {
 
 test_that("importFilterHypermutators correctly removes hypermutators", {
     # run importFilterHypermutators with a single hypermutator
-    testCNA <- readRDS('../../inst/extdata/devCNA.rds')
-    testSNV <- readRDS('../../inst/extdata/devSNV.rds')
+    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
-    readRDS('')
+    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)}