@@ -1194,6 +1194,18 @@ getDetails <- function(analysis, collection)

 }

+.loadPerts <- function(rp, coll) {

+    return(colnames(rp$get(coll)$ES))

+}

+

+.loadPEPs <- function(rp, coll, subset) {

+    peps <- list(

+        ES = rp$get(coll)$ES[, subset, drop=F],

+        PV = rp$get(coll)$PV[, subset, drop=F]

+    )

+    return(peps)

+}

+

 #' Performs Condition Set Enrichment Analysis

 #'

@@ -1276,10 +1288,10 @@ CondSEA <- function(rp_peps, pgset, bgset="all", collections="all",

     for(i in seq_along(dbs)) {        

         say(paste0("Working on collection: ", dbs[i]))

-        peps <- rp_peps$get(dbs[i])

+        allperts <- .loadPerts(rp, dbs[i])

         if(length(bgset) == 1 && bgset=="all")

-            bgset <- colnames(peps[[1]])

+            bgset <- allperts

         if(length(intersect(pgset, bgset))>0) {

             bgset <- setdiff(bgset, pgset)

@@ -1288,14 +1300,15 @@ CondSEA <- function(rp_peps, pgset, bgset="all", collections="all",

         rankingset <- c(bgset, pgset)

-        if(!all(rankingset %in% colnames(peps$ES)))

+        if(!all(rankingset %in% allperts))

             say(paste("The following conditions could not be found:",

                       paste(

                           setdiff(rankingset, colnames(peps$ES)),

                           collapse = ", ")), "error")

-        

+

+        peps <- .loadPEPs(rp_peps, dbs[i], rankingset)

         say(paste0("Row-ranking collection"))

-        ranked <- rankPEPsByRows(peps, rankingset)

+        ranked <- rankPEPsByRows(peps)

         say(paste0("Computing enrichments"))

         ks <- apply(ranked, 1, function(row) {

@@ -1458,7 +1471,7 @@ PathSEA <- function(rp_peps, pathways, bgsets="all", collections="all",

             say("Common pathway sets removed from bgset")

         }

         rankingset <- c(gmd, bgset)

-        peps <- rp_peps$get(collections[i])

+        peps <- .loadPEPs(rp_peps$get, collections[i])

         notok <- rankingset[rankingset %in% rownames(peps)]

         if(length(notok)>0)

             say(paste0("Pathway set ids not found in ", collections[i], ": ",

@@ -1733,12 +1746,9 @@ rankPEPsByCols <- function(peps, rankingset="all")

 }

-rankPEPsByRows <- function(peps, rankingset="all")

+rankPEPsByRows <- function(peps)

 {

-    if(length(rankingset) == 1 && rankingset == "all")

-        rankingset <- seq_len(ncol(peps[["ES"]]))

-

-    ESs <- peps[["ES"]][, rankingset, drop=FALSE]

+    ESs <- peps[["ES"]]

     x <- t(apply(-ESs, 1, rank, ties.method = "random", na.last="keep"))

     return(x)

 }

@@ -1906,3 +1916,9 @@ convertFromGSetClass <- function(gsets) {

     db_ids <- paste(dbs, subdbs, sep="_")

     return(db_ids)

 }

+

+.extractWorkingPEPs <- function(rp, coll, fgset, bgset) {

+    ishdf5 <- "#rhdf5" %in% rp$tags(coll)

+

+    

+}

@@ -135,6 +135,8 @@ oldpep2 <- rp$get(colls[2])

 rp$rm(tags="pep", force=T)

 importFromRawMode(rp)

+library(DelayedArray)

+

 pep2 <- list(ES=h5read(rp$get(colls[2]), "ES"),

              PV=h5read(rp$get(colls[2]), "PV"))

 rownames(pep2$ES) <- rownames(pep2$PV) <- h5read(rp$get(colls[2]), "rownames")

@@ -330,12 +332,10 @@ name3 <- colnames(testgep)[randj3]

 test_that("PathSEA", {

     expect_equal(getDetails(res, "c3_TFT"), res$details[["c3_TFT"]])   

     expect_equal(getResults(res, "c3_TFT"), res$PathSEA[["c3_TFT"]])   

-

     expect_equal(unname(res[["PathSEA"]][[db1]][name1, "ES"]),

                  ks1$ES)

     expect_equal(unname(res[["PathSEA"]][[db1]][name1, "PV"]),

                  ks1$p.value)

-

     expect_equal(unname(res[["PathSEA"]][[db3]][name3, "ES"]),

                  ks3$ES)

     expect_equal(unname(res[["PathSEA"]][[db3]][name3, "PV"]),