/usr/lib/R/site-library/affy/NAMESPACE is in r-bioc-affy 1.52.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 | useDynLib("affy")
importFrom(BiocGenerics, updateObject, colnames, boxplot, image)
import(affyio)
importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, MIAME,
Versioned, VersionedBiobase, Versions)
importClassesFrom(methods, ANY, character, environment, integer,
matrix, missing, numeric)
importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
assayData, classVersion, "classVersion<-",
description, "description<-", experimentData, exprs,
"exprs<-", featureNames, "featureNames<-",
isCurrent, isVersioned,
notes,
"notes<-", pData, "pData<-", phenoData,
"phenoData<-", preproc, "preproc<-", protocolData,
"protocolData<-", rowMedians, sampleNames, "sampleNames<-",
se.exprs, "se.exprs<-")
importMethodsFrom(methods, initialize, show)
importFrom(Biobase, addVigs2WinMenu, assayDataElementReplace,
assayDataNew, multiassign, read.AnnotatedDataFrame,
read.MIAME, testBioCConnection)
importMethodsFrom(BiocGenerics, normalize)
importFrom(BiocInstaller, biocinstallRepos)
importFrom(graphics, abline, axis, barplot, frame, hist,
lines, matplot, mtext, pairs, par, plot, points,
smoothScatter, text)
importFrom(grDevices, dev.interactive, gray)
importFrom(methods, as, callNextMethod, getMethod, is, new,
slot)
importFrom(preprocessCore, normalize.quantiles,
normalize.quantiles.robust, rma.background.correct)
importFrom(stats, approx, density, IQR, lm, loess, loess.control,
median, medpolish, model.response, model.weights, optim,
pnorm, predict, quantile, runif, sd, smooth.spline,
splinefun, t.test, terms, var, wilcox.test)
importFrom(utils, available.packages, contrib.url, data, flush.console,
install.packages, object.size)
##export everything that does not start with a .
exportPattern("^[^\\.]")
export(.setAffyOptions)
exportMethods(show, boxplot, image, exprs, featureNames, geneNames, sampleNames,
se.exprs, updateObject)
exportClasses("AffyBatch")
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