- 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.
... | ... |
@@ -1,6 +1,6 @@ |
1 | 1 |
Package: limma |
2 |
-Version: 3.41.15 |
|
3 |
-Date: 2019-07-24 |
|
2 |
+Version: 3.41.16 |
|
3 |
+Date: 2019-09-09 |
|
4 | 4 |
Title: Linear Models for Microarray Data |
5 | 5 |
Description: Data analysis, linear models and differential expression for microarray data. |
6 | 6 |
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 |
20 | 20 |
"pnorm", "ppoints", "predict", "pt", "qchisq", "qf", |
21 | 21 |
"qnorm", "qt", "quantile", "residuals", "rnorm", "sd", |
22 | 22 |
"uniroot", "var", "weighted.mean") |
23 |
-importFrom("utils", "getFromNamespace", "read.delim", "read.table", "write.table") |
|
23 |
+importFrom("utils", "getFromNamespace", "head", "read.delim", "read.table", "tail", "write.table") |
|
24 | 24 |
if( tools:::.OStype() == "windows" ) importFrom("utils", "winMenuAddItem") |
25 | 25 |
|
26 | 26 |
S3method("[",MAList) |
... | ... |
@@ -83,6 +83,12 @@ S3method(fitted,MArrayLM) |
83 | 83 |
S3method(fry,default) |
84 | 84 |
S3method(goana,default) |
85 | 85 |
S3method(goana,MArrayLM) |
86 |
+S3method(head,RGList) |
|
87 |
+S3method(head,MAList) |
|
88 |
+S3method(head,EListRaw) |
|
89 |
+S3method(head,EList) |
|
90 |
+S3method(head,MArrayLM) |
|
91 |
+S3method(head,TestResults) |
|
86 | 92 |
S3method(kegga,default) |
87 | 93 |
S3method(kegga,MArrayLM) |
88 | 94 |
S3method(labels,TestResults) |
... | ... |
@@ -130,4 +136,10 @@ S3method(plotDensities,RGList) |
130 | 136 |
S3method(plotDensities,MAList) |
131 | 137 |
S3method(plotDensities,EListRaw) |
132 | 138 |
S3method(plotDensities,EList) |
139 |
+S3method(tail,RGList) |
|
140 |
+S3method(tail,MAList) |
|
141 |
+S3method(tail,EListRaw) |
|
142 |
+S3method(tail,EList) |
|
143 |
+S3method(tail,MArrayLM) |
|
144 |
+S3method(tail,TestResults) |
|
133 | 145 |
S3method(unique,TestResults) |
... | ... |
@@ -1,4 +1,9 @@ |
1 |
-# CLASSES.R |
|
1 |
+# CLASSES.R |
|
2 |
+# This file defines data classes and extends standard base R methods to them. |
|
3 |
+# Other non-data classes are defined elsewhere in limma. See plotMDS.R for |
|
4 |
+# the "MDS" class, decideTests.R for the "TestResults" class and |
|
5 |
+# geneset-roast.R for the "Roast" class, |
|
6 |
+ |
|
2 | 7 |
|
3 | 8 |
setClass("RGList", |
4 | 9 |
# Class to hold initial read-in two-color data |
... | ... |
@@ -21,7 +26,7 @@ representation("list") |
21 | 26 |
) |
22 | 27 |
|
23 | 28 |
setClass("MArrayLM", |
24 |
-# Linear model fit |
|
29 |
+# Class to hold linear model fit |
|
25 | 30 |
representation("list") |
26 | 31 |
) |
27 | 32 |
|
... | ... |
@@ -251,3 +256,26 @@ as.data.frame.MArrayLM <- function(x, row.names = NULL, optional = FALSE, ...) |
251 | 256 |
} |
252 | 257 |
|
253 | 258 |
unique.TestResults <- function(x,...) unique([email protected],...) |
259 |
+ |
|
260 |
+head.RGList <- head.MAList <- head.EListRaw <- head.EList <- head.MArrayLM <- head.TestResults <- |
|
261 |
+function (x, n = 6L, ...) |
|
262 |
+{ |
|
263 |
+ stopifnot(length(n) == 1L) |
|
264 |
+ n <- if (n < 0L) |
|
265 |
+ max(nrow(x) + n, 0L) |
|
266 |
+ else |
|
267 |
+ min(n, nrow(x)) |
|
268 |
+ x[seq_len(n),] |
|
269 |
+} |
|
270 |
+ |
|
271 |
+tail.RGList <- tail.MAList <- tail.EListRaw <- tail.EList <- tail.MArrayLM <- tail.TestResults <- |
|
272 |
+function (x, n = 6L, ...) |
|
273 |
+{ |
|
274 |
+ stopifnot(length(n) == 1L) |
|
275 |
+ nrx <- nrow(x) |
|
276 |
+ n <- if (n < 0L) |
|
277 |
+ max(nrx + n, 0L) |
|
278 |
+ else |
|
279 |
+ min(n, nrx) |
|
280 |
+ x[seq.int(to = nrx, length.out = n),] |
|
281 |
+} |
... | ... |
@@ -1,3 +1,11 @@ |
1 |
+ 9 Sep 2019: limma 3.41.16 |
|
2 |
+ |
|
3 |
+- Update Users Guide: update Rsubread reference, correct remarks |
|
4 |
+ about prior distribution for 1/sigma^2 in Section 13.2 and rerun |
|
5 |
+ the Yoruba and Pasilla case studies. |
|
6 |
+ |
|
7 |
+- Add head() and tail() S3 methods for all limma data classes. |
|
8 |
+ |
|
1 | 9 |
24 July 2019: limma 3.41.15 |
2 | 10 |
|
3 | 11 |
- Add argument `gene.weights` to fry() so as to match the arguments |
5 | 13 |
new file mode 100644 |
... | ... |
@@ -0,0 +1,61 @@ |
1 |
+\name{head} |
|
2 |
+\alias{head.RGList} |
|
3 |
+\alias{head.MAList} |
|
4 |
+\alias{head.EListRaw} |
|
5 |
+\alias{head.EList} |
|
6 |
+\alias{head.MArrayLM} |
|
7 |
+\alias{head.TestResults} |
|
8 |
+\alias{tail.RGList} |
|
9 |
+\alias{tail.MAList} |
|
10 |
+\alias{tail.EListRaw} |
|
11 |
+\alias{tail.EList} |
|
12 |
+\alias{tail.MArrayLM} |
|
13 |
+\alias{tail.TestResults} |
|
14 |
+ |
|
15 |
+\title{Return the First to Last Part of a Data Object} |
|
16 |
+ |
|
17 |
+\description{ |
|
18 |
+Retrieve the first or last parts of an RGList, MAList, EListRaw, EList, MArrayLM or TestResults object. |
|
19 |
+} |
|
20 |
+ |
|
21 |
+\usage{ |
|
22 |
+\method{head}{EList}(x, n = 6L, \dots) |
|
23 |
+\method{tail}{EList}(x, n = 6L, \dots) |
|
24 |
+} |
|
25 |
+ |
|
26 |
+\arguments{ |
|
27 |
+ \item{x}{an object of class \code{RGList}, \code{MAList}, \code{EListRaw}, \code{EList}, \code{MArrayLM} or \code{TestResults}.} |
|
28 |
+ \item{n}{ |
|
29 |
+ a single integer. |
|
30 |
+ If positive or zero, number rows of resulting object. |
|
31 |
+ If negative, all but the \code{n} last/first rows of \code{x}. |
|
32 |
+ } |
|
33 |
+ \item{\dots}{other arguments are not currently used.} |
|
34 |
+} |
|
35 |
+ |
|
36 |
+\details{ |
|
37 |
+\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}. |
|
38 |
+} |
|
39 |
+ |
|
40 |
+\value{ |
|
41 |
+An object like \code{x} but generally with fewer rows. |
|
42 |
+} |
|
43 |
+ |
|
44 |
+\author{Gordon Smyth} |
|
45 |
+ |
|
46 |
+\seealso{ |
|
47 |
+ \code{\link{head}} in the utils package. |
|
48 |
+ |
|
49 |
+ \link{02.Classes} gives an overview of data classes used in LIMMA. |
|
50 |
+} |
|
51 |
+ |
|
52 |
+\examples{ |
|
53 |
+E <- matrix(rnorm(40),20,2) |
|
54 |
+rownames(E) <- paste0("Gene",1:20) |
|
55 |
+colnames(E) <- c("A","B") |
|
56 |
+y <- new("EList",list(E=E)) |
|
57 |
+head(y) |
|
58 |
+tail(y) |
|
59 |
+} |
|
60 |
+ |
|
61 |
+\keyword{array} |