add fold_change_int class

fold_change for interactions between factors

Author: grlloyd

.gitignore

@@ -13,3 +13,4 @@ inst/doc
 structtoolbox.Rproj
 *.Rproj
 *.Rproj
+*.tiff

DESCRIPTION

@@ -31,6 +31,7 @@ Collate:
     'filter_na_count.R'
     'filter_smeta_class.R'
     'fisher_exact_class.R'
+    'fold_change_int_class.R'
     'forward_selection_by_rank_class.R'
     'ggplot_theme_pub.R'
     'glog_class.R'

NAMESPACE

@@ -30,6 +30,7 @@ export(filter_na_count)
 export(filter_smeta)
 export(fisher_exact)
 export(fold_change)
+export(fold_change_int)
 export(fold_change_plot)
 export(forward_selection_byrank)
 export(fs_line)

R/fold_change_int_class.R

@@ -0,0 +1,50 @@
+#' fold change for interactions class
+#'
+#' calculates fold change between groups for all factors and interactions
+#'
+#' @import struct
+#' @import stats
+#' @export fold_change_int
+fold_change_int<-setClass(
+    "fold_change_int",
+    contains=c('method','fold_change'),
+)
+
+#' @export
+setMethod(f="method.apply",
+    signature=c("fold_change_int",'dataset'),
+    definition=function(M,D)
+    {
+
+        ## apply fold change between all pairwise combinations of levels of all factors
+        # combinations of factors
+        FF=structToolbox:::full_fact(M$factor_name)
+        FF=apply(FF,1,function(x) M$factor_name[x==1])
+        FF=FF[-1]
+
+        # remove single factor comparisons
+        L=lapply(FF,length)
+        w=which(L==1)
+        FF=FF[-w]
+
+        # for each combination create an interaction factor and compute fold-change on that factor
+        for (k in 1:length(FF))  {
+
+            D$sample_meta$interaction=interaction(D$sample_meta[,FF[[k]]])
+            FC=fold_change(alpha=M$alpha,paired=FALSE,sample_name='NA',factor_name='interaction')
+            FC=method.apply(FC,D)
+            if (k==1) {
+                M$fold_change=FC$fold_change
+                M$upper_ci=FC$upper_ci
+                M$lower_ci=FC$lower_ci
+            } else {
+                # bind the results tables together
+                M$fold_change=cbind(M$fold_change,FC$fold_change)
+                M$upper_ci=cbind(M$upper_ci,FC$upper_ci)
+                M$lower_ci=cbind(M$lower_ci,FC$lower_ci)
+            }
+        }
+
+        return(M)
+    }
+)