ensure correct order of outputs

in particular for paired tests, where additional features might be excluded

Author: grlloyd

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: structToolbox
 Type: Package
 Title: Data processing & analysis tools for Metabolomics and other omics
-Version: 1.5.4
+Version: 1.5.5
 Authors@R: c(
     person(
         c("Gavin","Rhys"),

R/ttest_class.R

@@ -165,7 +165,7 @@ setMethod(f="model_apply",
             y=D$sample_meta[[M$factor_names]]
 
             # sort the data by sample id so that theyre in the right order for paired ttest
-            temp=D$sample_meta[order(D$sample_meta[[M$factor_names]],D$sample_meta[[M$paired_factor]]),]
+            temp=D$sample_meta[order(D$sample_meta[[M$factor_names]],D$sample_meta[[M$paired_factor]]), ]
             D=D[rownames(temp),]
 
             # check number per class
@@ -224,6 +224,8 @@ setMethod(f="model_apply",
         output=merge(temp,as.data.frame(t(output),stringsAsFactors = FALSE),by=0,all=TRUE,sort=FALSE)
         rownames(output)=output$Row.names
         output=output[,-1]
+        # ensure outputs are in the correct order (TODO: update to data.frame with rownames)
+        output=output[CN,]
         output$p.value=p.adjust(output$p.value,method = param_value(M,'mtc'))
         output_value(M,'t_statistic')=output$statistic.t
         output_value(M,'p_value')=output$p.value

R/wilcox_test_class.R

@@ -99,7 +99,7 @@ setMethod(f="model_apply",
         y=D$sample_meta[[M$factor_names]]
         L=levels(y)
         if (length(L)!=2) {
-            stop('must have exactly two levels for this implmentation of t-statistic')
+            stop('must have exactly two levels for this implementation of t-statistic')
         }
 
         if (M$paired){
@@ -128,7 +128,7 @@ setMethod(f="model_apply",
             D=D[!(D$sample_meta[[M$paired_factor]] %in% out),]
             y=D$sample_meta[[M$factor_names]]
 
-            # sort the data by sample id so that theyre in the right order for paired ttest
+            # sort the data by sample id so that they're in the right order for paired ttest
             temp=D$sample_meta[order(D$sample_meta[[M$factor_names]],D$sample_meta[[M$paired_factor]]),]
             D=D[rownames(temp),]
 
@@ -154,6 +154,8 @@ setMethod(f="model_apply",
         output=merge(temp,as.data.frame(t(output),stringsAsFactors = FALSE),by=0,all=TRUE,sort=FALSE)
         rownames(output)=output$Row.names
         output=output[,-1]
+        # ensure outputs are in the correct order (TODO: update to data.frame with rownames)
+        output=output[CN,]
         output$p.value=p.adjust(output$p.value,method = param_value(M,'mtc'))
         if (M$paired) {
             output_value(M,'statistic')=output$statistic.V