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

 Package: DEsubs

-Version: 1.7.1

+Version: 1.7.2

 Date: 2017-07-23

 Title: DEsubs: an R package for flexible identification of

         differentially expressed subpathways using RNA-seq expression

@@ -25,7 +25,7 @@ Repository: Bioconductor

 Date/Publication:

 NeedsCompilation: no

 LazyLoad: yes

-Imports: graph, igraph, RBGL, circlize, limma, edgeR, samr, EBSeq,

+Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq,

         NBPSeq, DESeq, stats, grDevices, graphics, pheatmap, utils,

         ggplot2, Matrix, jsonlite, tools, DESeq2, methods

 Suggests: RUnit, BiocGenerics, knitr

@@ -11,8 +11,8 @@ importFrom( 'DESeq2',

                 'estimateDispersions',

                 'nbinomWaldTest',

                 'results')

-importFrom( 'samr', 

-                'SAMseq' )

+

+

 importFrom( 'limma', 

                 'voom', 

                 'lmFit', 

@@ -60,7 +60,7 @@ DEsubs <- function( org, mRNAexpr, mRNAnomenclature, pathways,

     if ( missing(classes) )      { message('Please supply the classes.') }

     if ( missing(DEGchoice) )    { message('Please supply a type.') }

-    supportedMethods <- c('edgeR', 'DESeq', 'EBSeq', 'samr', 'NBPSeq', 

+    supportedMethods <- c('edgeR', 'DESeq', 'EBSeq', 'NBPSeq', 

                             'voom+limma', 'vst+limma', 'TSPM')

     if ( DEGchoice == 'edgeR' )

@@ -116,34 +116,34 @@ DEsubs <- function( org, mRNAexpr, mRNAnomenclature, pathways,

         return(adjpvalues)

     }

-    if ( DEGchoice == 'samr' )

-    {

-        # samr

-        sink( tempfile() ) 

-        SAMseq.test <- suppressMessages(SAMseq(count.matrix, classes, 

-                            resp.type="Two class unpaired", 

-                            geneid = rownames(count.matrix), 

-                            genenames = rownames(count.matrix),

-                            nperms = 100, nresamp = 20, fdr.output = 1))

-        SAMseq.result.table <- rbind( 

-                            SAMseq.test[['siggenes.table']][['genes.up']], 

-                            SAMseq.test[['siggenes.table']][['genes.lo']])

-        SAMseq.score        <- rep(0,  nrow(count.matrix))

-        idx                 <- match(SAMseq.result.table[,1], 

-                                    rownames(count.matrix))

-        SAMseq.score[idx]   <- as.numeric(SAMseq.result.table[,3])

-        SAMseq.FDR          <- rep(1, nrow(count.matrix))

-        idx                 <- match(SAMseq.result.table[,1], 

-                                    rownames(count.matrix)) 

-        SAMseq.FDR[idx]     <- as.numeric(SAMseq.result.table[,5])/100

-        adjpvalues          <- SAMseq.FDR

-        genes               <- SAMseq.result.table[, 'Gene ID']

-        names(adjpvalues)   <- genes

+    # if ( DEGchoice == 'samr' )

+    # {

+    #     # samr

+    #     sink( tempfile() ) 

+    #     SAMseq.test <- suppressMessages(SAMseq(count.matrix, classes, 

+    #                         resp.type="Two class unpaired", 

+    #                         geneid = rownames(count.matrix), 

+    #                         genenames = rownames(count.matrix),

+    #                         nperms = 100, nresamp = 20, fdr.output = 1))

+    #     SAMseq.result.table <- rbind( 

+    #                         SAMseq.test[['siggenes.table']][['genes.up']], 

+    #                         SAMseq.test[['siggenes.table']][['genes.lo']])

+    #     SAMseq.score        <- rep(0,  nrow(count.matrix))

+    #     idx                 <- match(SAMseq.result.table[,1], 

+    #                                 rownames(count.matrix))

+    #     SAMseq.score[idx]   <- as.numeric(SAMseq.result.table[,3])

+    #     SAMseq.FDR          <- rep(1, nrow(count.matrix))

+    #     idx                 <- match(SAMseq.result.table[,1], 

+    #                                 rownames(count.matrix)) 

+    #     SAMseq.FDR[idx]     <- as.numeric(SAMseq.result.table[,5])/100

+    #     adjpvalues          <- SAMseq.FDR

+    #     genes               <- SAMseq.result.table[, 'Gene ID']

+    #     names(adjpvalues)   <- genes

-        sink()

+    #     sink()

-        return(adjpvalues)

-    }

+    #     return(adjpvalues)

+    # }

     if ( DEGchoice == 'EBSeq' )

     {

         # run EBSeq

@@ -1,3 +1,6 @@

+1.7.2   - Removed 'Significance Analysis of Microarrays' (SAM) from 

+            available differential expression analysis options due to the 

+            removal of its package from the ecosystem.

 1.3.4:  - Fixing (persistent) inconsistencies between vignette output within

 			the package and the output in the landing page.

@@ -17,7 +17,7 @@ or a filename of a text file stored in the 'User' directory.}

     'hgnc_transcript_name', 'refseq_mrna', 'refseq_peptide')}

 \item{pathways}{Pathway type ('All', 'Non-Metabolic', 'Metabolic')}

 \item{DEtool}{DEG analysis tool selection for NodeRule ('edgeR', 'DESeq', 

-    'EBSeq', 'samr', 'NBPSeq', 'voom+limma', 'vst+limma', 'TSPM')}

+    'EBSeq', 'NBPSeq', 'voom+limma', 'vst+limma', 'TSPM')}

 \item{DEpar}{DE analysis tools Q-value threshold of NodeRule 

     (default: DEGpar = 0.05)}

 \item{CORtool}{ Correlation measure selection for EdgeRule 

@@ -203,12 +203,12 @@ Supported Labels                                    R command

 [@leng2013ebseq]                                    'EBSeq'

 [@smyth2004linear]                                  'vst+limma'

 [@anders2010differential]; [@smyth2004linear]       'voom+limma'

-[@li2013finding]                                    'samr'

 [@di2011nbp]                                        'NBPSeq'

 [@auer2011two]                                      'TSPM'

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

 Table: Node Rule options

+\newpage

 ## 5. Subpathway Extraction