310 Index
object.size(), 24
objects(), 23
old.packages(), 217
oldClass(), 79, 84
oldClass<-(), 79
on.exit(), 54
OOP, 7
options(), 46, 47
order(), 152
ordered(), 18
package
aaMI, 145
annotate, 145, 265
AnnotationDbi, 243, 244, 248,
250, 252, 253
base, 57, 58, 110, 212, 216, 224,
225
Biobase, 4, 46, 73, 78, 104, 108,
150, 169, 216, 222, 223, 226,
232–234, 245
biocViews, 211, 218
biomaRt, 144, 229, 265–268
Biostrings, 141, 145, 166, 171,
173, 174, 177, 181, 197
BSgenome, 172
codetools, 273, 276, 277
ctv, 211
datasets, 212
DBI, 238, 240
flowCore, 3
genefilter, 234
geneplotter, 159
GeneR, 145
GEOquery, 270
GO.db, 248, 252
graph, 89, 110, 115, 117, 218
graphics, 212, 215
grDevices, 212
grid, 65
hgu95av2, 230
hgu95av2.db, 244, 248
JRI, 210
KEGG, 272
KEGG.db, 252
KEGGSOAP, 272
lattice, 65, 215
limma, 218
MASS, 58
matchprobes, 145, 172, 175
methods, 100, 101, 212, 220
odfWeave, 215
pkg, 223
pkgDepTools, 218
PROcess, 3
RBGL, 115, 218
RBioinf, 87, 111, 115, 121, 134,
186, 192, 193, 198, 199, 201,
203, 208, 223, 241, 242, 258,
275, 278, 281
RCurl, 143
RdbiPgSQL, 238
relax, 215
Rgraphviz, 115, 116, 218
RIntact, 258
rJava, 210
Rlibstree, 170, 181
RMySQL, 238
RODBC, 238
ROracle, 238
RPy, 210
RSJava, 210
RSPerl, 210
RSPython, 209, 210
RSQLite, 238
seqinR, 145
SQLite, 239, 241
SSOAP, 272
stats, 120, 188, 189, 212
Sxslt, 254
tools, 216, 217, 226
utils, 212, 215
weaver, 215
XML, 257, 261, 264
xtable, 155
package authoring, 219
package basics, 212
package data, 215
package events, 227
package management, 216
Chapter 9. Index 311
package.dependencies(), 217
package.skeleton(), 219
packageDescription(), 214
packageEvent(), 227
packages, 211
packageStartupMessage(), 226
parent.frame(), 53
parse, 158
parse(), 142
parsing HTML, 263
paste(), 41, 148, 155, 172, 242
path.expand(), 126, 127
pdf(), 65
Perl, 1
pipe(), 134, 135
pkgDepends(), 217
pkgVignettes(), 216
plot(), 71, 103
plot.Foo(), 81
pm.abstGrep(), 265
pm.getabst(), 265
pmatch(), 153, 154
png(), 65
pnorm(), 199
p olymorphism, 67, 70
popHUMANCHIPDB(), 253
popMOUSECHIPDB(), 253
postscript(), 65
ppc(), 234
print(), 55, 80, 130, 140, 156, 159,
216, 274
print(x)(), 274
print.FreqFlyer(), 71
print.Passenger(), 71
printWithNumbers(), 142, 285
processingInstruction(), 257
prod(), 15, 83
prompt(), 221
promptClass(), 111, 221, 223
promptMethods(), 111, 221, 223
promptPackage(), 221
PROTECT, 194
protect, 196
prototype, 85, 90
prototype(), 90
PubMed, 265
pubmed(), 265
pushBack(), 131
Python, 1
Q(), 274
qnorm(), 199
quote(), 55, 207
R.home(), 120
randDNA(), 151
random numbers, 199
range(), 83
rapply(), 232, 233
rbind(), 234
Rcal(), 135
Rd format, 223
read.csv(), 138
read.csv2(), 138
read.dcf(), 140, 141
read.delim(), 130, 138
read.delim2(), 138
read.table(), 17, 138, 139
readBin(), 140
readChar(), 140
readFASTA(), 141, 142
readLines(), 121, 130, 131, 134, 137,
141
recover(), 273, 275, 279, 280
recursive, 18
recycling rule, 37
Reduce(), 39
regexp(), 160
regexpr(), 160, 165
regular expression, 159, 160, 233
removeClass(), 86
removeGeneric(), 103
removeMethod(), 105
removeMethods(), 105
repeat(), 42, 43
replacement function, 38, 83, 147
replacement method, 107
reproducible research, 215
require(), 213, 227
reshape(), 235
312 Index
return(), 41
rev(), 172
reverseSeq(), 172
reverseSplit(), 245, 246
revmap(), 245, 246
Rkeys(), 244
rm(), 6
rm(e1)(), 21, 22
rma(), 297, 298
Rmemprof(), 298
Rmlfun(), 61
RNGkind(), 201, 202
rnorm(), 13, 199
round(), 83
rowFtests(), 234
rowMax(), 234
rowMeans(), 234
rowMin(), 234
rowpAUCs(), 234
rowQ(), 234
rowrep(), 39
rowrep(x, 4) = c(11, 12)(), 39
rowSums(), 192, 234
rowttests(), 234
Rprof(), 290, 294
Rprofmem(), 295
runif(), 13, 292
Ruuid(), 125
S3 classes, 7, 74, 100, 101, 113
S3 dispatch, 81
S3 generic functions, 7, 78, 80
S3 methods, 114
S4 classes, 85, 100, 197, 223
S4 methods, 114
S4Help(), 111, 223
sample(), 13
sapply(), 231–233, 260
save(), 129, 130
scale(), 42
scan(), 121, 131, 137, 142
sealClass(), 98
search(), 23, 213
search path, 23, 51, 58, 101, 108, 212,
219, 220, 224, 225
seek(), 136, 137
self join, 243
sep(), 127
seq(), 13, 30, 31
seq_along(), 13
seq_len(), 13
sessionInfo(), 23, 24, 213
set.seed(), 3, 201
setAs(), 89, 90
setClass(), 85, 94, 95, 98, 99, 111
setClassUnion(), 99
setdiff(), 272
setGeneric(), 101, 102, 114
setHook(), 227
setIs(), 98, 108
setMethod(), 71, 101, 103, 105, 106,
110, 114
setOldClass(), 74, 88, 100, 101, 112
setReplaceMethod(), 107
setRepositories(), 217
setValidity(), 94
setVNames(), 275, 281
setwd(), 120, 122, 123
show(), 71, 159
showConnections(), 130
showMethods(), 90
signature, 69, 101
signif(), 83
simplePVect(), 192
simpleRand(), 186, 198, 202
simpleSort(), 186, 198, 199
sin(), 83
single(), 191
single dispatch, 69
single inheritance, 68
sinh(), 83
sink(), 132, 133, 142, 143
sink.number(), 143
slotNames(), 87
SOAP, 272
sort(), 292
sort.int(), 292
sorting, 152, 199
source(), 142
sp ecial values, 8, 189
Chapter 9. Index 313
split(), 231
sprintf(), 155
stack(), 235
standardGeneric(), 101
startDocument(), 257
startElement(), 257
startIndex(), 177
stop(), 46
storage.mode(), 10
str(), 24
strbreak(), 150
strsplit(), 127, 144, 149, 152, 160,
172
strtrim(), 150, 159, 297
strwhite(), 168
strwrap(), 150, 159
sub(), 152, 160, 264
subclass, 68
subClassNames(), 87
subset assignment, 29
subsetAsCharacter(), 287, 288
substitute(), 53
substr(), 147, 148
substring(), 147, 148
sux tree, 169
sum(), 15, 83
summary(), 130
summaryRprof(), 290, 294
superclass, 68, 70
superClassNames(), 87
suppressPackageStartupMessages(),
226
Sweave(), 150, 215, 216
sweep(), 42
switch(), 44, 45
sys.frame(), 53
sys.frame(sys.parent())(), 53
Sys.getlocale(), 152, 159
Sys.info(), 22
sys.parent(), 53
Sys.setlocale(), 159
Sys.sleep(), 134
system(), 125, 135
system.file(), 120–122, 141, 157,
214, 216, 248
system.time(), 292
table(), 153, 231, 236
tail(), 24, 125
tan(), 83
tanh(), 83
tapply(), 232
tempdir(), 125
tempfile(), 125, 126
testBioCConnection(), 46
text(), 257
textConnection(), 131
tolower(), 151
toTable(), 244
toupper(), 151
trace(), 112, 142, 273, 279, 285–288
traceback(), 278
tracemem(), 298
TRUE(), 44, 139, 191
trunc(), 83
try(), 3, 46, 47, 124, 278
tryCatch(), 3, 46–49, 124, 278
typeof(), 10, 11, 24
unclass(), 17
undebug(), 281, 285
unlink(), 128, 129, 136
unstack(), 235
untrace(), 285, 287
unz(), 130
update.packages(), 210
url(), 143
url.show(), 143
URLdecode(), 143
URLencode(), 143
UseMethod(), 7, 78, 79, 81, 103, 114
validity, 85, 94
validObject(), 95
vignette, 215
vignette(), 215, 216
virtual class, 85, 98
warning(), 46
web service, 272
314 Index
wget(), 144
while(), 42, 43
with(), 54
withCallingHandlers(), 49, 279
write(), 140
write.csv(), 140
write.csv2(), 140
write.dcf(), 140, 141
write.table(), 140
write.tlp(), 225
writeBin(), 140
writeChar(), 140
writeFASTA(), 141
writeLines(), 137
X11(), 65
XML, 254
XML event parsing, 261
XML handlers, 257, 258
XML name space, 255, 258, 259
XML parsing, 265
xmlApply(), 261, 266
xmlAttr(), 260
xmlEventParse(), 257
xmlGetAttr(), 263
xmlNamespaceDefinitions(), 258
xmlTreeParse(), 257, 258
xmlValue(), 260
XPath, 256, 259, 263
xpathApply(), 261

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