@@ -2,7 +2,7 @@ Package: TCC

 Type: Package

 Title: TCC: Differential expression analysis for tag count data with

         robust normalization strategies

-Version: 1.20.0

+Version: 1.20.1

 Author: Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, and Koji Kadota

 Maintainer: Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp>, Tomoaki

         Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>

@@ -21,7 +21,6 @@ Description: This package provides a series of functions for performing

         virtue of the use of combinations of functions in depended

         packages.

 Depends: R (>= 2.15), methods, DESeq, DESeq2, edgeR, baySeq, ROC

-Imports: samr

 Suggests: RUnit, BiocGenerics

 Enhances: snow

 License: GPL-2

@@ -33,8 +33,6 @@ importFrom(edgeR, topTags)

-# import methods from samr

-importFrom(samr, SAMseq)

 # import methods from baySeq

@@ -74,13 +74,13 @@ TCC <- setRefClass(

             private$paired <<- FALSE

             private$available$norm.method <<- c("tmm", "deseq", "deseq2")

             private$available$test.method <<- data.frame(

-                TGY  = c(T, T, T, T, T, T),  # ID:1 (two-group)

-                TGN  = c(T, T, T, T, F, F),  # ID:1 (two-group without replicate)

-                TGNP = c(T, T, T, T, T, T),  # ID:4 (paired two-group)

-                MGY  = c(T, T, T, T, T, T),  # ID:2 (three-group)

-                MGN  = c(T, T, T, T, F, F),  # ID:2 (three-group without replicate)

-                MF   = c(T, T, T, T, F, T),  # ID:3 (multi-factors)

-                row.names = c("bayseq", "deseq", "deseq2", "edger", "samseq", "voom")

+                TGY  = c(T, T, T, T, T),  # ID:1 (two-group)

+                TGN  = c(T, T, T, T, F),  # ID:1 (two-group without replicate)

+                TGNP = c(T, T, T, T, T),  # ID:4 (paired two-group)

+                MGY  = c(T, T, T, T, T),  # ID:2 (three-group)

+                MGN  = c(T, T, T, T, F),  # ID:2 (three-group without replicate)

+                MF   = c(T, T, T, T, T),  # ID:3 (multi-factors)

+                row.names = c("bayseq", "deseq", "deseq2", "edger", "voom")

             )

         }

     )

@@ -168,7 +168,6 @@ TCC$methods(calcNormFactors = function(norm.method = NULL,

                    "deseq2" = .self$.testByDeseq2(...),

                    "bayseq" = .self$.testByBayseq(...),

                    "voom" = .self$.testByLimmavoom(...),

-                   "samseq" = .self$.testBySamseq(...),

                    "wad" = .self$.testByWad(...),

                    #"yayoi" = .self$.testByYayoi(norm = TRUE, ...),

                    stop(paste("\nTCC::ERROR: The identifying method of ", test.method, " doesn't supported.\n"))

@@ -136,9 +136,6 @@ TCC$methods(estimateDE = function (test.method = NULL,

                                           bgroup     = bayseq.group,

                                           paired     = paired,

                                           ...),

-           "samseq" = .self$.testBySamseq(samplesize = samplesize,

-                                          paired     = paired,

-                                          ...),

            "voom" = .self$.testByLimmavoom(design = design, 

                                            coef   = coef, 

                                            paired = paired,

@@ -1,3 +1,5 @@

+if (FALSE) {

+

 TCC$methods(.testBySamseq = function(...) {

 if(! requireNamespace("samr", quietly=TRUE)) {

@@ -79,4 +81,4 @@ switch(test.approach,

 })

-

+}

@@ -32,7 +32,7 @@ The estimated normalization factors obtained by using the

 \code{\link{calcNormFactors}} function are used within the statistical

 model for differential analysis in the \code{\link{estimateDE}} function.

 Both two functions internally call functions from other packages

-(edgeR, DESeq, baySeq, EBSeq, and samr) when specified.

+(edgeR, DESeq, baySeq, and EBSeq) when specified.

 TCC also provides some useful functions: \code{\link{simulateReadCounts}}

 for generating simulation data with various experimental designs,

 \code{\link{plot}} for depicting a M-A plot,

@@ -30,7 +30,7 @@ The procedure can generally be described as the

     \item{test.method}{character specifying a method for identifying

           differentially expressed genes (DEGs) used in \eqn{STEP2}:

           one of \code{"edger"}, \code{"deseq"}, \code{"deseq2"},

-          \code{"bayseq"}, \code{"samseq"}, \code{"voom"} and \code{"wad"}.

+          \code{"bayseq"}, \code{"voom"} and \code{"wad"}.

           See the "Details" filed in \code{\link{estimateDE}} for detail.

           The default is \code{"edger"} when analyzing the count data with

           multiple replicates (i.e., \code{min(table(tcc$group[, 1])) > 1}),

@@ -24,7 +24,7 @@ implemented in other R packages.

     \item{test.method}{character string specifying a method for identifying

           DEGs: one of \code{"edger"}, \code{"deseq"}, \code{"deseq2"},

-          \code{"bayseq"}, \code{"samseq"}, \code{"voom"}, and \code{"wad"}.

+          \code{"bayseq"}, \code{"voom"}, and \code{"wad"}.

           See the "Details" field for detail.

           The default is \code{"edger"} when analyzing the count data with

           replicates (i.e., \code{min(table(tcc$group[, 1])) > 1}), and

@@ -82,9 +82,7 @@ implemented in other R packages.

           for details.}

     \item{samplesize}{integer specifying (i) the sample size for estimating the

-          prior parameters if \code{test.method = "bayseq"} (defaults to 10000),

-          and (ii) the number of permutation in samr if

-          \code{test.method = "samseq"} (defaults to 100).}

+          prior parameters if \code{test.method = "bayseq"} (defaults to 10000).}

     \item{logged}{logical. If \code{TRUE}, the input data are regarded as 

           log2-transformed. If \code{FALSE}, the log2-transformation is

@@ -157,12 +155,6 @@ packages are internally called according to the specified

           If \code{paired = TRUE}, 

           \code{\link[baySeq]{getPriors}} and

           \code{\link[baySeq]{getLikelihoods}} in baySeq are used.

-    \item \code{test.method = "samseq"}\cr

-          \code{\link[samr]{SAMseq}} with

-          \code{resp.type = "Two class unpaired"} arugment

-          in samr package is called to identify DEGs for two-group data,

-          \code{resp.type = "Two class paired"} for paired two-group data,

-          and \code{resp.type = "Multiclass"} for multi-group data.

     \item \code{test.method = "voom"}\cr

           \code{\link[limma]{voom}}, \code{\link[limma]{lmFit}}, and

           \code{\link[limma]{eBayes}} in limma are internally called