started hitlist intersection

R/bio/cummerutils.R

@@ -31,3 +31,41 @@ guess_mart <- function(gene_id){
     }
 }
 #guess_mart("ENSCAFG00000000043")
+
+
+
+### Hit List Interscection Utilitities (see e.g Helin project for examples)
+
+
+
+extractHits <- function(s1, s2, s1Overexpressed=T, degData=degs){
+  # note one of the two sets will always be empty; Example:  s1="small_cyst"; s2="liver_polar_stage1"
+  forward <- subset(degData, sample_1==s1 & sample_2==s2 & sample_1_overex==s1Overexpressed)$ensembl_gene_id %>% ac()
+  reverse <- subset(degData, sample_1==s2 & sample_2==s1 & sample_1_overex==!s1Overexpressed)$ensembl_gene_id %>% ac()
+
+  return(c(forward, reverse))
+}
+
+
+s1_gt_s2 <- function(s1, s2, ...) extractHits(s1, s2, s1Overexpressed=T, ...)
+s1_lt_s2 <- function(s1, s2, ...) extractHits(s1, s2, s1Overexpressed=F, ...)
+s1_ne_s2 <- function(s1, s2, ...) c(extractHits(s1, s2, s1Overexpressed=F, ...), extractHits(s1, s2, s1Overexpressed=T, ...))
+
+
+## todo add helper to test for equality (s1 and s2 not differentially expressed)
+## from marta:
+#s1_eq_s2 <- function(s1, s2, degData=degs) subset(degData, sample_1==s1 & sample_2==s2 & sample_1_overex==F)$gene_id
+#AeqBexpr <-subset(allDiff, sample_1=="aRG" & sample_2=="bRG") %>% filter(pmin(value_1, value_2)>1) %>% filter(!isHit)
+#hitdata <- rbind(hitdata, data.frame(ensembl_gene_id=AeqBexpr$gene_id, set="aRG==bRG"))
+
+
+rintersect <- function(...){
+    LDF <- list(...)
+    rec_intersect <- LDF[[1]]
+    for (i in 2:length(LDF)) {
+        rec_intersect <- intersect(rec_intersect, LDF[[i]])
+    }
+    rec_intersect
+}
+
+