@@ -1,7 +1,7 @@

 Package: gep2pep

 Type: Package

 Title: Creation and Analysis of Pathway Expression Profiles (PEPs)

-Version: 0.99.2.2

+Version: 0.99.2.3

 Date: 2017-09-11

 Author: Francesco Napolitano <franapoli@gmail.com>

 Maintainer: Francesco Napolitano <franapoli@gmail.com>

@@ -384,6 +384,8 @@ importFromRawMode <- function(rp, path=file.path(rp$root(), "raw"),

       say("\nDone.")

   }

+

+    H5close()

 }

 #' Imports pathways data from an MSigDB XML file.

@@ -1221,10 +1223,24 @@ getDetails <- function(analysis, collection)

 }

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

-    peps <- list(

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

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

-    )

+    ish5 <- "#hdf5" %in% rp$tags(coll)

+

+    if(ish5) {

+        if(missing(subset))

+            subset <- NULL

+        fname <- rp$get(coll)

+        data <- h5read(fname, "ES-PV", index=list(NULL, subset))

+        peps <- list(

+            ES = data[1:(nrow(data)/2),],

+            PV = data[(nrow(data)/2 + 1):nrow(data),]

+        )        

+    } else {

+        peps <- list(

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

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

+        )

+    }

+    

     return(peps)

 }

@@ -1,10 +1,10 @@

 ## Workflow:

-library(GSEABase)

-library(devtools)

-library(testthat)

-load_all()

+## library(GSEABase)

+## library(devtools)

+## library(testthat)

+## load_all()

 dbfolder <- file.path(tempdir(), "gep2pepDB")

@@ -135,10 +135,10 @@ oldpep2 <- rp$get(colls[2])

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

 importFromRawMode(rp)

-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")

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

+pep2 <- gep2pep::.loadPEPs(rp, colls[2])

+

+rownames(pep2$ES) <- rownames(pep2$PV) <- rp$get(colls[2])

+colnames(pep2$ES) <- colnames(pep2$PV) <- rp$get(colls[2])

 ## rownames(pep2$ES)

 ##  [1] "M7785"  "M6394"  "M18759" "M10635" "M14709" "M4820"  "M7677"  "M11751"

@@ -152,10 +152,10 @@ colnames(pep2$ES) <- colnames(pep2$PV) <- h5read(rp$get(colls[2]), "colnames")

 test_that("check hdf5 PEPss", {

     expect_true(all(oldpep2$ES==pep2$ES))

     expect_true(all(oldpep2$PV==pep2$PV))

-    expect_true(all(rownames(oldpep2$ES)==rownames(pep2$ES)))

-    expect_true(all(rownames(oldpep2$PV)==rownames(pep2$PV)))

-    expect_true(all(colnames(oldpep2$ES)==colnames(pep2$ES)))

-    expect_true(all(colnames(oldpep2$PV)==colnames(pep2$PV)))

+    expect_true(all(rownames(oldpep2$ES) == rownames(pep2$ES)))

+    expect_true(all(rownames(oldpep2$PV) == rownames(pep2$PV)))

+    expect_true(all(colnames(oldpep2$ES) == colnames(pep2$ES)))

+    expect_true(all(colnames(oldpep2$PV) == colnames(pep2$PV)))

 })

 res <- list()