1. ClassifyR
  2. Commit fa5ddb645654bd2add4cf5d451b49dbf120c4dcc
Browse code

- Fixed remainder of old-format parameter construction in examples and a couple of typos.

Dario Strbenac authored on 22/08/2022 05:30:05
Showing 5 changed files
R/plotFeatureClasses.R
History View file @ fa5ddb64
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@@ -384,7 +384,7 @@ setMethod("plotFeatureClasses", "MultiAssayExperiment",
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               )
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             }
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-            MultiAssayExperiment::colData(measurements) <- MultiAssayExperiment::colData(measurements)[colnames(MultiAssayExperiment::colData(measurements)) %in% sampleInfouseFeatures[, 2]]
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+            MultiAssayExperiment::colData(measurements) <- MultiAssayExperiment::colData(measurements)[colnames(MultiAssayExperiment::colData(measurements)) %in% clinicalUseFeatures[, 2]]
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             measurements <- MultiAssayExperiment::wideFormat(measurements, colDataCols = seq_along(MultiAssayExperiment::colData(measurements)), check.names = FALSE, collapse = ':')
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             measurements <- measurements[, -1, drop = FALSE] # Remove sample IDs.
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             S4Vectors::mcols(measurements)[, "sourceName"] <- gsub("colDataCols", "clinical", S4Vectors::mcols(measurements)[, "sourceName"])
R/runTest.R
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@@ -59,7 +59,7 @@
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 #'   #{
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 #'     data(asthma)
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 #'     tuneList <- list(nFeatures = seq(5, 25, 5), performanceType = "Balanced Error")
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-#'     selectParams <- SelectParams(limmaRanking, tuneParams = tuneList)
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+#'     selectParams <- SelectParams("limma", tuneParams = tuneList)
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 #'     modellingParams <- ModellingParams(selectParams = selectParams)
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 #'     trainIndices <- seq(1, nrow(measurements), 2)
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 #'     testIndices <- seq(2, nrow(measurements), 2)
R/runTests.R
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@@ -48,7 +48,7 @@
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 #'
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 #'     CVparams <- CrossValParams(permutations = 5)
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 #'     tuneList <- list(nFeatures = seq(5, 25, 5), performanceType = "Balanced Error")
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-#'     selectParams <- SelectParams(differentMeansRanking, tuneParams = tuneList)
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+#'     selectParams <- SelectParams("t-test", tuneParams = tuneList)
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 #'     modellingParams <- ModellingParams(selectParams = selectParams)
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 #'     runTests(measurements, classes, CVparams, modellingParams,
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 #'              DataFrame(characteristic = c("Assay Name", "Classifier Name"),
man/runTest.Rd
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@@ -102,7 +102,7 @@ perform each iteration.
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   #{
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     data(asthma)
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     tuneList <- list(nFeatures = seq(5, 25, 5), performanceType = "Balanced Error")
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-    selectParams <- SelectParams(limmaRanking, tuneParams = tuneList)
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+    selectParams <- SelectParams("limma", tuneParams = tuneList)
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     modellingParams <- ModellingParams(selectParams = selectParams)
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     trainIndices <- seq(1, nrow(measurements), 2)
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     testIndices <- seq(2, nrow(measurements), 2)
man/runTests.Rd
History View file @ fa5ddb64
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@@ -77,7 +77,7 @@ parallel is possible by leveraging the package \code{\link{BiocParallel}}.
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     CVparams <- CrossValParams(permutations = 5)
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     tuneList <- list(nFeatures = seq(5, 25, 5), performanceType = "Balanced Error")
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-    selectParams <- SelectParams(differentMeansRanking, tuneParams = tuneList)
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+    selectParams <- SelectParams("t-test", tuneParams = tuneList)
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     modellingParams <- ModellingParams(selectParams = selectParams)
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     runTests(measurements, classes, CVparams, modellingParams,
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              DataFrame(characteristic = c("Assay Name", "Classifier Name"),