fix broken examples

Author: grlloyd

R/filter_smeta_class.R

@@ -8,7 +8,7 @@
 #' @param factor_name the sample_meta column name to use
 #'
 #' @examples
-#' D = sbcms_data()
+#' D = sbcms_dataset()
 #' M = filter_smeta(mode='exclude',levels='QC',factor_name='QC')
 #' M = method.apply(M,D)
 #'

R/fold_change_class.R

@@ -4,7 +4,7 @@
 #' a log transform and t-test.
 #'
 #' @examples
-#' D = sbcms_data()
+#' D = sbcms_dataset()
 #' M = fold_change(factor_name='class')
 #' M = method.apply(M,D)
 #'

R/fold_change_int_class.R

@@ -4,8 +4,10 @@
 #' factors. Note that paired forced to FALSE for all comparisons.
 #'
 #' @examples
-#' D = sbcms_data()
-#' M = fold_change_int(factor_name=c('class','batch'))
+#' D = sbcms_dataset()
+#' D$data=D$data[,1:10,drop=FALSE]
+#' M = filter_smeta(mode='exclude',levels='QC',factor_name='class') +
+#'     fold_change_int(factor_name=c('class','batch'))
 #' M = method.apply(M,D)
 #'
 #' @param alpha confidence level to use for intervals
@@ -20,6 +22,7 @@
 fold_change_int<-setClass(
     "fold_change_int",
     contains=c('method','fold_change'),
+    prototype = list(predicted='fold_change')
 )
 
 #' @export
@@ -30,7 +33,7 @@ setMethod(f="method.apply",
 
         ## apply fold change between all pairwise combinations of levels of all factors
         # combinations of factors
-        FF=structToolbox:::full_fact(M$factor_name)
+        FF=full_fact(M$factor_name)
         FF=apply(FF,1,function(x) M$factor_name[x==1])
         FF=FF[-1]
 

R/ttest_class.R

@@ -14,7 +14,7 @@ ttest<-setClass(
         params.mtc='entity.stato',
         params.factor_names='entity',
         params.paired='entity',
-        params.paired_factor='character',
+        params.paired_factor='entity',
         # OUTPUTS
         outputs.t_statistic='entity.stato',
         outputs.p_value='entity',
@@ -52,6 +52,11 @@ ttest<-setClass(
             type='logical',
             description='TRUE/FALSE to apply paired t-test.'
         ),
+        params.paired_factor=entity(name='Paired factor',
+            value='NA',
+            type='character',
+            description='Factor name that encodes the sample id for pairing'
+        ),
         outputs.t_statistic=entity.stato(name='t-statistic',
             stato.id='STATO:0000176',
             type='numeric',