diff w4mclassfilter_wrapper.R @ 8:d5cf23369d12 draft

planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1

--- a/w4mclassfilter_wrapper.R	Mon Jan 29 21:20:07 2018 -0500
+++ b/w4mclassfilter_wrapper.R	Sat Mar 03 22:58:14 2018 -0500
@@ -82,6 +82,7 @@
 
 # other parameters
 
+transformation <- as.character(argVc["transformation"])
 wildcards <- as.logical(argVc["wildcards"])
 sampleclassNames <- as.character(argVc["sampleclassNames"])
 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]]
@@ -96,6 +97,42 @@
 variable_range_filter <- as.character(argVc["variable_range_filter"])
 variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]]
 
+## -----------------------------
+## Transformation and imputation
+## -----------------------------
+my_w4m_filter_imputation <- if (transformation == "log10") {
+  function(m) {
+    if (!is.matrix(m))
+      stop("Cannot impute and transform data - the supplied data is not in matrix form")
+    if (nrow(m) == 0)
+      stop("Cannot impute and transform data - data matrix has no rows")
+    if (ncol(m) == 0)
+      stop("Cannot impute and transform data - data matrix has no columns")
+    suppressWarnings(
+      # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step
+      m <- log10(m)
+    )
+    return ( w4m_filter_imputation(m) )
+  }
+} else if (transformation == "log2") {
+  function(m) {
+    if (!is.matrix(m))
+      stop("Cannot impute and transform data - the supplied data is not in matrix form")
+    if (nrow(m) == 0)
+      stop("Cannot impute and transform data - data matrix has no rows")
+    if (ncol(m) == 0)
+      stop("Cannot impute and transform data - data matrix has no columns")
+    suppressWarnings(
+      # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step
+      m <- log2(m)
+    )
+    return ( w4m_filter_imputation(m) )
+  }
+} else {
+  # use the method from the w4mclassfilter class
+  w4m_filter_imputation
+}
+
 ##------------------------------
 ## Computation
 ##------------------------------
@@ -113,6 +150,7 @@
 , samplename_column     = samplenameColumn
 , variable_range_filter = variable_range_filter
 , failure_action        = my_print
+, data_imputation       = my_w4m_filter_imputation
 )
 
 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",