In generateMapSnvSel change read.csv2 to read.csv

KrasnitzLab · Aug 31, 2024 · 930b62d · 930b62d
1 parent 79712a4
commit 930b62d
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Showing 5 changed files with 14 additions and 15 deletions.
diff --git a/R/process1KG.R b/R/process1KG.R
@@ -197,8 +197,8 @@ generateMapSnvSel <- function(cutOff=0.01, fileSNV, fileSNPsRDS, fileFREQ) {
     }
 
     ## Read the bulk SNP information file
-    mapSNVSel <- read.csv2(fileSNV)
-
+    # mapSNVSel <- read.csv2(fileSNV)
+    mapSNVSel <- read.csv(fileSNV)
     ## Identify SNPs that have a frequency equal or superior to the cut-off
     ## in at least one super population
     listSNP <- which(rowSums(mapSNVSel[,c("EAS_AF",

diff --git a/inst/extdata/matFreqSNV_Demo.txt.bz2 b/inst/extdata/matFreqSNV_Demo.txt.bz2
diff --git a/man/RAIDS-package.Rd b/man/RAIDS-package.Rd
diff --git a/tests/testthat/fixtures/matFreqSNV_Demo.txt.bz2 b/tests/testthat/fixtures/matFreqSNV_Demo.txt.bz2
diff --git a/tests/testthat/test-process1KG.R b/tests/testthat/test-process1KG.R
@@ -173,18 +173,18 @@ test_that("generateMapSnvSel() must generate expected output", {
                                         54489, 54707, 54715),
                             REF=c("T", "T", "C", "G", "G", "G", "C"),
                             ALT=c("G", "A", "A", "A", "A", "C", "T"),
-                            AF=as.character(c(0.02, 0.11, 0.08, 0.07,
-                                                0.1, 0.23, 0.21)),
-                            EAS_AF=c("0.0", "0.0", "0.05", "0.01",
-                                     "0.0", "0.08", "0.07"),
-                            EUR_AF=c("0.04", "0.2", "0.12", "0.14",
-                                     "0.18", "0.38", "0.34"),
-                            AFR_AF=c("0.03", "0.02", "0.05", "0.06",
-                                     "0.02", "0.18", "0.16"),
-                            AMR_AF=c("0.03", "0.12", "0.06", "0.07",
-                                     "0.1", "0.25", "0.24"),
-                            SAS_AF=c("0.02", "0.22", "0.1", "0.09",
-                                      "0.21", "0.28", "0.27"),
+                            AF=c(0.02, 0.11, 0.08, 0.07,
+                                0.1, 0.23, 0.21),
+                            EAS_AF=c(0.0, 0.0, 0.05, 0.01,
+                                     0.0, 0.08, 0.07),
+                            EUR_AF=c(0.04, 0.2, 0.12, 0.14,
+                                     0.18, 0.38, 0.34),
+                            AFR_AF=c(0.03, 0.02, 0.05, 0.06,
+                                     0.02, 0.18, 0.16),
+                            AMR_AF=c(0.03, 0.12, 0.06, 0.07,
+                                     0.1, 0.25, 0.24),
+                            SAS_AF=c(0.02, 0.22, 0.1, 0.09,
+                                      0.21, 0.28, 0.27),
                             stringsAsFactors = FALSE)
 
     expect_equivalent(readRDS(filterSNVFile), snpFilteredExpected)