@@ -81,7 +81,7 @@ isRdsFile <- function(file)

         return(FALSE)

     if (!is(file, "character"))

         return(FALSE)

-    return(tools::file_ext(file) == ".rds")

+    return(tools::file_ext(file) == "rds")

 }

 #' get input that might be an RDS file

new file mode 100755

Binary files /dev/null and b/tests/testthat/temp_params.rds differ

@@ -200,5 +200,22 @@ test_that("Valid Top-Level CoGAPS Calls",

     res <- CoGAPS(gistCsvPath, nIterations=100, outputFrequency=100, seed=42,

         messages=FALSE, nPatterns=3, subsetIndices=1:100, subsetDim=1)

     expect_true(nrow(res@featureLoadings) == 100)

+

+    # test using RDS file for parameters

+    matP <- getSampleFactors(GIST.result)

+    params <- CogapsParams(nPatterns=ncol(matP), nIterations=175, seed=42,

+        singleCell=TRUE, sparseOptimization=TRUE, distributed="genome-wide",

+        explicitSets=list(1:200, 201:400, 401:600, 601:800, 801:1000))

+    params <- setDistributedParams(params, nSets=5, cut=ncol(matP) + 1)

+    params <- setFixedPatterns(params, matP, "P")

+    saveRDS(params, file="temp_params.rds")

+

+    res1 <- CoGAPS(GIST.matrix, params)

+    res2 <- CoGAPS(GIST.matrix, "temp_params.rds")

+    

+    expect_true(all(res1@featureLoadings == res2@featureLoadings))

+    expect_true(all(res1@featureStdDev == res2@featureStdDev))

+    expect_true(all(res1@sampleFactors == res2@sampleFactors))

+    expect_true(all(res1@sampleStdDev== res2@sampleStdDev))

 })