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

 Package: limma

-Version: 3.35.3

-Date: 2017-12-03

+Version: 3.35.4

+Date: 2017-12-13

 Title: Linear Models for Microarray Data

 Description: Data analysis, linear models and differential expression for microarray data.

 Author: Gordon Smyth [cre,aut], Yifang Hu [ctb], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Davis McCarthy [ctb], Di Wu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Aaron Lun [ctb], Natalie Thorne [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Yunshun Chen [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]

@@ -84,6 +84,8 @@ S3method(goana,default)

 S3method(goana,MArrayLM)

 S3method(kegga,default)

 S3method(kegga,MArrayLM)

+S3method(labels,TestResults)

+S3method(levels,TestResults)

 S3method(merge,MAList)

 S3method(merge,RGList)

 S3method(merge,EList)

@@ -10,7 +10,9 @@ summary.TestResults <- function(object,...)

 	if(is.null(Levels)) Levels <- c(-1L,0L,1L)

 	nlevels <- length(Levels)

 	tab <- matrix(0L,nlevels,ncol(object))

-	dimnames(tab) <- list(as.character(Levels),colnames(object))

+	Labels <- attr(object,"labels")

+	if(is.null(Labels)) Labels <- as.character(Levels)

+	dimnames(tab) <- list(Labels,colnames(object))

 	for (i in 1:nlevels) tab[i,] <- colSums(object==Levels[i],na.rm=TRUE)

 	class(tab) <- "table"

 	tab

@@ -21,12 +23,18 @@ setMethod("show","TestResults",function(object) {

 	printHead([email protected])

 })

+levels.TestResults <- function(x) attr(x,"levels")

+

+labels.TestResults <- function(object,...) attr(object,"labels")

+

+

 decideTests <- function(object,...) UseMethod("decideTests")

 decideTests.default <- function(object,method="separate",adjust.method="BH",p.value=0.05,lfc=0,coefficients=NULL,cor.matrix=NULL,tstat=NULL,df=Inf,genewise.p.value=NULL,...)

 #	Accept or reject hypothesis tests across genes and contrasts

+#	from a matrix of p-values

 #	Gordon Smyth

-#	17 Aug 2004. Last modified 8 Jan 2017.

+#	17 Aug 2004. Last modified 13 Dec 2017.

 {

 	method <- match.arg(method,c("separate","global","hierarchical","nestedF"))

 	if(method=="nestedF") stop("nestedF adjust method requires an MArrayLM object",call.=FALSE)

@@ -82,8 +90,10 @@ decideTests.default <- function(object,method="separate",adjust.method="BH",p.va

 	if(is.null(coefficients)) coefficients <- tstat

 	if(is.null(coefficients)) {

 		attr(isDE,"levels") <- c(0L,1L)

+		attr(isDE,"labels") <- c("NotSig","Sig")

 	} else {

 		attr(isDE,"levels") <- c(-1L,0L,1L)

+		attr(isDE,"labels") <- c("Down","NotSig","Up")

 		coefficients <- as.matrix(coefficients)

 		if( !all(dim(coefficients)==dim(p)) ) stop("dim(object) disagrees with dim(coefficients)")

 		i <- coefficients<0

@@ -97,7 +107,7 @@ decideTests.default <- function(object,method="separate",adjust.method="BH",p.va

 decideTests.MArrayLM <- function(object,method="separate",adjust.method="BH",p.value=0.05,lfc=0,...)

 #	Accept or reject hypothesis tests across genes and contrasts

 #	Gordon Smyth

-#	17 Aug 2004. Last modified 8 Jan 2017.

+#	17 Aug 2004. Last modified 13 Dec 2017.

 {

 	if(is.null(object$p.value)) object <- eBayes(object)

 	method <- match.arg(method,c("separate","global","hierarchical","nestedF"))

@@ -154,6 +164,8 @@ decideTests.MArrayLM <- function(object,method="separate",adjust.method="BH",p.v

 		else

 			[email protected] <- [email protected] * (abs(object$coefficients)>lfc)

 	}

+	attr(results,"levels") <- c(-1L,0L,1L)

+	attr(results,"labels") <- c("Down","NotSig","Up")

 	results

 }

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

+13 Dec 2017: limma 3.35.4

+

+- "TestResults" objects now include a 'labels' attribute, defaulting

+  to c("Down","NotSig","Up").

+

  3 Dec 2017: limma 3.35.3

 - New arguments 'quote' and 'row.names' for write.fit(). Write.fit()

@@ -3,6 +3,8 @@

 \alias{TestResults-class}

 \alias{show,TestResults-method}

 \alias{summary.TestResults}

+\alias{levels.TestResults}

+\alias{labels.TestResults}

 \title{Matrix of Test Results - class}

 \description{

@@ -12,10 +14,12 @@ A matrix-based class for storing the results of simultanous tests.

 \usage{

 \S3method{summary}{TestResults}(object, \dots)

+\S3method{labels}{TestResults}(object, \dots)

+\S3method{levels}{TestResults}(x)

 }

 \arguments{

-\item{object}{object of class \code{TestResults}}

+\item{object, x}{object of class \code{TestResults}}

 \item{\dots}{other arguments are not used}

 }

@@ -46,8 +50,8 @@ Functions in LIMMA which operate on \code{TestResults} objects include

 }

 \examples{\dontrun{

-#  Assume a data object MA and a design matrix

-fit <- lmFit(MA, design)

+#  Assume a data object y and a design matrix

+fit <- lmFit(y, design)

 fit <- eBayes(fit)

 results <- decideTests(fit)

 summary(results)