@@ -1,5 +1,5 @@

 Package: DEsubs

-Version: 1.13.0

+Version: 1.13.1

 Date: 2017-07-23

 Title: DEsubs: an R package for flexible identification of

         differentially expressed subpathways using RNA-seq expression

@@ -2,7 +2,7 @@

                                 pathways='all')

 {

     # If a filename is given, read a text file from the 'User' directory.

-    if ( class(mRNAexpr) == 'character' )

+    if ( is(mRNAexpr, 'character') )

     {

         dir <- paste0(cache[['baseDir']], '//User') 

         mRNAexpr <- readLines(paste(dir, mRNAexpr, sep='//'))

@@ -43,9 +43,9 @@

     edgeList[idx] <- lapply(edgeList[idx], as.character)

     pathIds <- as.numeric(edgeList[, 4])

-    if ( pathways == 'Metabolic')

+    if ( 'Metabolic' %in% pathways )

         { edgeList <- edgeList[which(pathIds < 2000), ] }

-    if ( pathways == 'Non-Metabolic')

+    if ( 'Non-Metabolic' %in% pathways )

         { edgeList <- edgeList[which(pathIds >= 2000), ] }

     # Filter edgelist with gene within the RNA-seq data

@@ -91,7 +91,7 @@

     if ( !is.null(rankedList) )

     {

         # A filepath is given as input

-        if ( class(rankedList) != 'numeric')

+        if ( !is(rankedList, 'numeric') ) 

         {

             file <- rankedList

             rankedList.data <- read.table(file, dec = '.', sep=' ')

@@ -101,7 +101,7 @@

         # A ranked list of differentially expressed genes is given as input,

         # in the form of a named vector, storing the Q-values and the gene

         # names (the vector's names).

-        if ( class(rankedList) == 'numeric')

+        if ( is(rankedList, 'numeric') ) 

         { 

             genes <- rankedList 

         }

@@ -50,7 +50,8 @@

     if (is.null(limat))     { return(limat) }

     # If input is already a matrix, return original data.

-    if (class(limat) == 'matrix') { return(limat) }

+    if ( is(limat, 'matrix') )  

+        { return(limat) }

     # Find what type of data the list holds

     type <- NULL

@@ -1,3 +1,8 @@

+CHANGES IN VERSION 1.13.1

+------------------------

+

+    - Updates for _R_CHECK_LENGTH_1_LOGIC2_, _R_CHECK_LENGTH_1_CONDITION_, classEq.

+

 CHANGES IN VERSION 1.9.1

 ------------------------