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

 Package: limma

-Version: 3.41.15

-Date: 2019-07-24

+Version: 3.41.16

+Date: 2019-09-09

 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]

@@ -20,7 +20,7 @@ importFrom("stats", "approx", "approxfun", "as.dendrogram", "as.dist", "cmdscale

            "pnorm", "ppoints", "predict", "pt", "qchisq", "qf",

            "qnorm", "qt", "quantile", "residuals", "rnorm", "sd",

            "uniroot", "var", "weighted.mean")

-importFrom("utils", "getFromNamespace", "read.delim", "read.table", "write.table")

+importFrom("utils", "getFromNamespace", "head", "read.delim", "read.table", "tail", "write.table")

 if( tools:::.OStype() == "windows" ) importFrom("utils", "winMenuAddItem")

 S3method("[",MAList)

@@ -83,6 +83,12 @@ S3method(fitted,MArrayLM)

 S3method(fry,default)

 S3method(goana,default)

 S3method(goana,MArrayLM)

+S3method(head,RGList)

+S3method(head,MAList)

+S3method(head,EListRaw)

+S3method(head,EList)

+S3method(head,MArrayLM)

+S3method(head,TestResults)

 S3method(kegga,default)

 S3method(kegga,MArrayLM)

 S3method(labels,TestResults)

@@ -130,4 +136,10 @@ S3method(plotDensities,RGList)

 S3method(plotDensities,MAList)

 S3method(plotDensities,EListRaw)

 S3method(plotDensities,EList)

+S3method(tail,RGList)

+S3method(tail,MAList)

+S3method(tail,EListRaw)

+S3method(tail,EList)

+S3method(tail,MArrayLM)

+S3method(tail,TestResults)

 S3method(unique,TestResults)

@@ -1,4 +1,9 @@

-#	CLASSES.R

+#  CLASSES.R

+#  This file defines data classes and extends standard base R methods to them.

+#  Other non-data classes are defined elsewhere in limma. See plotMDS.R for

+#  the "MDS" class, decideTests.R for the "TestResults" class and

+#  geneset-roast.R for the "Roast" class,

+

 setClass("RGList",

 #  Class to hold initial read-in two-color data

@@ -21,7 +26,7 @@ representation("list")

 )

 setClass("MArrayLM",

-#  Linear model fit

+#  Class to hold linear model fit

 representation("list")

 )

@@ -251,3 +256,26 @@ as.data.frame.MArrayLM <- function(x, row.names = NULL, optional = FALSE, ...)

 }

 unique.TestResults <- function(x,...) unique([email protected],...)

+

+head.RGList <- head.MAList <- head.EListRaw <- head.EList <- head.MArrayLM <- head.TestResults <-

+function (x, n = 6L, ...) 

+{

+	stopifnot(length(n) == 1L)

+	n <- if (n < 0L) 

+		max(nrow(x) + n, 0L)

+	else

+		min(n, nrow(x))

+	x[seq_len(n),]

+}

+

+tail.RGList <- tail.MAList <- tail.EListRaw <- tail.EList <- tail.MArrayLM <- tail.TestResults <-

+function (x, n = 6L, ...) 

+{

+	stopifnot(length(n) == 1L)

+	nrx <- nrow(x)

+	n <- if (n < 0L) 

+		max(nrx + n, 0L)

+	else

+		min(n, nrx)

+	x[seq.int(to = nrx, length.out = n),]

+}

@@ -1,3 +1,11 @@

+ 9 Sep 2019: limma 3.41.16

+

+- Update Users Guide: update Rsubread reference, correct remarks

+  about prior distribution for 1/sigma^2 in Section 13.2 and rerun

+  the Yoruba and Pasilla case studies.

+

+- Add head() and tail() S3 methods for all limma data classes.

+

 24 July 2019: limma 3.41.15

 - Add argument `gene.weights` to fry() so as to match the arguments

Binary files a/inst/doc/usersguide.pdf and b/inst/doc/usersguide.pdf differ

new file mode 100644

@@ -0,0 +1,61 @@

+\name{head}

+\alias{head.RGList}

+\alias{head.MAList}

+\alias{head.EListRaw}

+\alias{head.EList}

+\alias{head.MArrayLM}

+\alias{head.TestResults}

+\alias{tail.RGList}

+\alias{tail.MAList}

+\alias{tail.EListRaw}

+\alias{tail.EList}

+\alias{tail.MArrayLM}

+\alias{tail.TestResults}

+

+\title{Return the First to Last Part of a Data Object}

+

+\description{

+Retrieve the first or last parts of an RGList, MAList, EListRaw, EList, MArrayLM or TestResults object.

+}

+

+\usage{

+\method{head}{EList}(x, n = 6L, \dots)

+\method{tail}{EList}(x, n = 6L, \dots)

+}

+

+\arguments{

+  \item{x}{an object of class \code{RGList}, \code{MAList}, \code{EListRaw}, \code{EList}, \code{MArrayLM} or \code{TestResults}.}

+  \item{n}{

+    a single integer.

+    If positive or zero, number rows of resulting object.

+    If negative, all but the \code{n} last/first rows of \code{x}.

+  }

+  \item{\dots}{other arguments are not currently used.}

+}

+

+\details{

+\code{head} (\code{tail}) returns the first (last) \code{n} rows when \code{n >= 0} or all but the last (first) \code{n} rows when \code{n < 0}.

+}

+

+\value{

+An object like \code{x} but generally with fewer rows.

+}

+

+\author{Gordon Smyth}

+

+\seealso{

+  \code{\link{head}} in the utils package.

+  

+  \link{02.Classes} gives an overview of data classes used in LIMMA.

+}

+

+\examples{

+E <- matrix(rnorm(40),20,2)

+rownames(E) <- paste0("Gene",1:20)

+colnames(E) <- c("A","B")

+y <- new("EList",list(E=E))

+head(y)

+tail(y)

+}

+

+\keyword{array}