/usr/lib/R/site-library/limma/NAMESPACE is in r-bioc-limma 3.34.0+dfsg-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 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 | # All functions exported other than those starting with "."
exportPattern("^[^\\.]")
exportClasses("RGList","MAList","EListRaw","EList","MArrayLM","TestResults","LargeDataObject","Roast","MDS")
exportMethods("show")
import(methods)
importFrom("grDevices", "col2rgb", "dev.cur", "dev.off", "png", "rgb")
importFrom("graphics", "abline", "axis", "barplot", "coplot", "image",
"legend", "lines", "matplot", "mtext", "panel.smooth",
"par", "plot", "plot.new", "points", "polygon", "rect",
"segments", "text", "title")
importFrom("stats", "approx", "approxfun", "as.dendrogram", "as.dist", "cmdscale",
"coef", "contr.sum", "contrasts<-", "cov", "cov2cor",
"dist", "density", "df", "dhyper", "dnorm", "filter", "fitted",
"hat", "hclust", "integrate", "isoreg", "lm", "lm.fit", "lm.wfit", "loess",
"lowess", "median", "model.matrix", "na.exclude", "na.omit",
"nlminb", "nls", "nls.control", "optim", "p.adjust",
"pbeta", "pchisq", "pexp", "pf", "pgamma", "phyper",
"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")
if( tools:::.OStype() == "windows" ) importFrom("utils", "winMenuAddItem")
S3method("[",MAList)
S3method("[",MArrayLM)
S3method("[",RGList)
S3method("[",EList)
S3method("[",EListRaw)
S3method(anova,MAList)
S3method(as.data.frame,EList)
S3method(as.data.frame,EListRaw)
S3method(as.data.frame,MAList)
S3method(as.data.frame,MArrayLM)
S3method(as.matrix,MAList)
S3method(as.matrix,EList)
S3method(as.matrix,EListRaw)
S3method(as.matrix,MArrayLM)
S3method(as.matrix,marrayNorm)
S3method(as.matrix,PLMset)
S3method(as.matrix,RGList)
S3method(as.matrix,ExpressionSet)
S3method(as.matrix,LumiBatch)
S3method(as.matrix,vsn)
S3method(avedups,default)
S3method(avedups,MAList)
S3method(avedups,EList)
S3method(avereps,default)
S3method(avereps,RGList)
S3method(avereps,MAList)
S3method(avereps,EListRaw)
S3method(avereps,EList)
S3method(avearrays,default)
S3method(avearrays,MAList)
S3method(avearrays,EList)
S3method(camera,default)
S3method(cameraPR,default)
S3method(cbind,MAList)
S3method(cbind,RGList)
S3method(cbind,EList)
S3method(cbind,EListRaw)
S3method(decideTests,default)
S3method(decideTests,MArrayLM)
S3method(detectionPValues,default)
S3method(detectionPValues,EListRaw)
S3method(dim,MAList)
S3method(dim,MArrayLM)
S3method(dim,RGList)
S3method(dim,EList)
S3method(dim,EListRaw)
S3method(dimnames,MAList)
S3method(dimnames,MArrayLM)
S3method(dimnames,RGList)
S3method(dimnames,EList)
S3method(dimnames,EListRaw)
S3method("dimnames<-",MAList)
S3method("dimnames<-",RGList)
S3method("dimnames<-",EList)
S3method("dimnames<-",EListRaw)
S3method(fitted,MArrayLM)
S3method(fry,default)
S3method(goana,default)
S3method(goana,MArrayLM)
S3method(kegga,default)
S3method(kegga,MArrayLM)
S3method(merge,MAList)
S3method(merge,RGList)
S3method(merge,EList)
S3method(merge,EListRaw)
S3method(mroast,default)
S3method(roast,default)
S3method(romer,default)
S3method(rbind,MAList)
S3method(rbind,RGList)
S3method(rbind,EList)
S3method(rbind,EListRaw)
S3method(residuals,MArrayLM)
S3method(summary,MAList)
S3method(summary,MArrayLM)
S3method(summary,RGList)
S3method(summary,EList)
S3method(summary,EListRaw)
S3method(summary,TestResults)
S3method(normalizeVSN,default)
S3method(normalizeVSN,RGList)
S3method(normalizeVSN,EListRaw)
S3method(plotMA,default)
S3method(plotMA,RGList)
S3method(plotMA,MAList)
S3method(plotMA,EListRaw)
S3method(plotMA,EList)
S3method(plotMA,MArrayLM)
S3method(plotMD,default)
S3method(plotMD,RGList)
S3method(plotMD,MAList)
S3method(plotMD,EListRaw)
S3method(plotMD,EList)
S3method(plotMD,MArrayLM)
S3method(plotMDS,default)
S3method(plotMDS,MDS)
S3method(plotFB,default)
S3method(plotFB,RGList)
S3method(plotFB,EListRaw)
S3method(plotDensities,default)
S3method(plotDensities,RGList)
S3method(plotDensities,MAList)
S3method(plotDensities,EListRaw)
S3method(plotDensities,EList)
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