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| 139 | </style> | 139 | </style> |
| 140 | <link·rel="stylesheet"·href="https://cdn.jsdelivr.net/npm/katex/dist/katex.min.css"> | 140 | <link·rel="stylesheet"·href="https://cdn.jsdelivr.net/npm/katex/dist/katex.min.css"> |
| 141 | </head> | 141 | </head> |
| 142 | <body> | 142 | <body> |
| 143 | <div·class="frontmatter"> | 143 | <div·class="frontmatter"> |
| 144 | <div·class="title"><h1>Making·and·Utilizing·TxDb·Objects</h1></div> | 144 | <div·class="title"><h1>Making·and·Utilizing·TxDb·Objects</h1></div> |
| 145 | <div·class="author"><h2>Marc·Carlson,·Patrick·Aboyoun,·Hervé·Pagès,·Seth·Falcon,·Martin·Morgan</h2></div> | 145 | <div·class="author"><h2>Marc·Carlson,·Patrick·Aboyoun,·Hervé·Pagès,·Seth·Falcon,·Martin·Morgan</h2></div> |
| 146 | <div·class="date"><h3> | 146 | <div·class="date"><h3>Friday,·June·07,·2024</h3></div> |
| 147 | </div> | 147 | </div> |
| 148 | <div·class="body"> | 148 | <div·class="body"> |
| 149 | <h2·id="introduction">Introduction</h2> | 149 | <h2·id="introduction">Introduction</h2> |
| 150 | <p>The·<code>GenomicFeatures</code>·package·retrieves·and·manages | 150 | <p>The·<code>GenomicFeatures</code>·package·retrieves·and·manages |
| 151 | transcript-related·features·from·the·UCSC·Genome | 151 | transcript-related·features·from·the·UCSC·Genome |
| 152 | Bioinformatics\footnote{(<a·href="https://genome.ucsc.edu/)%7D">https://genome.ucsc.edu/)}</a>·and | 152 | Bioinformatics\footnote{(<a·href="https://genome.ucsc.edu/)%7D">https://genome.ucsc.edu/)}</a>·and |
| 153 | BioMart\footnote{(<a·href="http://www.biomart.org/)%7D">http://www.biomart.org/)}</a>·data·resources.·The | 153 | BioMart\footnote{(<a·href="http://www.biomart.org/)%7D">http://www.biomart.org/)}</a>·data·resources.·The |
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| 234 | to·the·seqlevels·stored·in·the·db),·then·set·the·seqlevels·to | 234 | to·the·seqlevels·stored·in·the·db),·then·set·the·seqlevels·to |
| 235 | <code>seqlevels0(txdb)</code>.</p> | 235 | <code>seqlevels0(txdb)</code>.</p> |
| 236 | <pre><code·class="language-r">seqlevels(txdb)·<-·seqlevels0(txdb) | 236 | <pre><code·class="language-r">seqlevels(txdb)·<-·seqlevels0(txdb) |
| 237 | </code></pre> | 237 | </code></pre> |
| 238 | <pre><code>##·Error·in·seqlevels0(txdb):·could·not·find·function·"seqlevels0" | 238 | <pre><code>##·Error·in·seqlevels0(txdb):·could·not·find·function·"seqlevels0" |
| 239 | </code></pre> | 239 | </code></pre> |
| 240 | <p>\begin{Exercise}·Use·</code>seqlevels<code>·to·set·only·chromsome·15·to·be·active.··BTW,·the·rest·of·this·vignette·will·assume·you·have·succeeded·at·this.·\end{Exercise} | 240 | <p>\begin{Exercise}·Use·</code>seqlevels<code>·to·set·only·chromsome·15·to·be·active.··BTW,·the·rest·of·this·vignette·will·assume·you·have·succeeded·at·this.·\end{Exercise} |
| 241 | ` | 241 | `Ej\begin{Solution}</p> |
| 242 | <pre><code·class="language-r">seqlevels(txdb)·<-·"chr15" | 242 | <pre><code·class="language-r">seqlevels(txdb)·<-·"chr15" |
| 243 | </code></pre> | 243 | </code></pre> |
| 244 | <pre><code>##·Error:·object·'txdb'·not·found | 244 | <pre><code>##·Error:·object·'txdb'·not·found |
| 245 | </code></pre> | 245 | </code></pre> |
| 246 | <pre><code·class="language-r">seqlevels(txdb) | 246 | <pre><code·class="language-r">seqlevels(txdb) |
| 247 | </code></pre> | 247 | </code></pre> |
| 248 | <pre><code>##·Error·in·seqlevels(txdb):·could·not·find·function·"seqlevels" | 248 | <pre><code>##·Error·in·seqlevels(txdb):·could·not·find·function·"seqlevels" |
| 249 | </code></pre> | 249 | </code></pre> |
| 250 | <p>\end{Solution} | 250 | <p>\end{Solution}Ej`</p> |
| 251 | <h3·id="retrieving-data-using-the-select-method">Retrieving·data·using·the·select·method</h3> | 251 | <h3·id="retrieving-data-using-the-select-method">Retrieving·data·using·the·select·method</h3> |
| 252 | <p>The·<code>TxDb</code>·objects·inherit·from·<code>AnnotationDb</code> | 252 | <p>The·<code>TxDb</code>·objects·inherit·from·<code>AnnotationDb</code> |
| 253 | objects·(just·as·the·<code>ChipDb</code>·and·<code>OrgDb</code>·objects·do). | 253 | objects·(just·as·the·<code>ChipDb</code>·and·<code>OrgDb</code>·objects·do). |
| 254 | One·of·the·implications·of·this·relationship·is·that·these·object | 254 | One·of·the·implications·of·this·relationship·is·that·these·object |
| 255 | ought·to·be·used·in·similar·ways·to·each·other.··Therefore·we·have | 255 | ought·to·be·used·in·similar·ways·to·each·other.··Therefore·we·have |
| 256 | written·supporting·<code>columns</code>,·<code>keytypes</code>,·<code>keys</code> | 256 | written·supporting·<code>columns</code>,·<code>keytypes</code>,·<code>keys</code> |
| 257 | and·<code>select</code>·methods·for·<code>TxDb</code>·objects.</p> | 257 | and·<code>select</code>·methods·for·<code>TxDb</code>·objects.</p> |
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| 270 | <pre><code>##·Error·in·keytypes(txdb):·could·not·find·function·"keytypes" | 270 | <pre><code>##·Error·in·keytypes(txdb):·could·not·find·function·"keytypes" |
| 271 | </code></pre> | 271 | </code></pre> |
| 272 | <pre><code·class="language-r">select(txdb,·keys·=·keys,·columns="TXNAME",·keytype="GENEID") | 272 | <pre><code·class="language-r">select(txdb,·keys·=·keys,·columns="TXNAME",·keytype="GENEID") |
| 273 | </code></pre> | 273 | </code></pre> |
| 274 | <pre><code>##·Error·in·select(txdb,·keys·=·keys,·columns·=·"TXNAME",·keytype·=·"GENEID"):·could·not·find·function·"select" | 274 | <pre><code>##·Error·in·select(txdb,·keys·=·keys,·columns·=·"TXNAME",·keytype·=·"GENEID"):·could·not·find·function·"select" |
| 275 | </code></pre> | 275 | </code></pre> |
| 276 | <p>\begin{Exercise}·For·the·genes·in·the·example·above,·find·the·chromosome·and·strand·information·that·will·go·with·each·of·the·transcript·names.·\end{Exercise} | 276 | <p>\begin{Exercise}·For·the·genes·in·the·example·above,·find·the·chromosome·and·strand·information·that·will·go·with·each·of·the·transcript·names.·\end{Exercise} |
| 277 | ` | 277 | `Ej\begin{Solution}</p> |
| 278 | <pre><code·class="language-r">columns(txdb) | 278 | <pre><code·class="language-r">columns(txdb) |
| 279 | </code></pre> | 279 | </code></pre> |
| 280 | <pre><code>##·Error·in·columns(txdb):·could·not·find·function·"columns" | 280 | <pre><code>##·Error·in·columns(txdb):·could·not·find·function·"columns" |
| 281 | </code></pre> | 281 | </code></pre> |
| 282 | <pre><code·class="language-r">cols·<-·c("TXNAME",·"TXSTRAND",·"TXCHROM") | 282 | <pre><code·class="language-r">cols·<-·c("TXNAME",·"TXSTRAND",·"TXCHROM") |
| 283 | select(txdb,·keys=keys,·columns=cols,·keytype="GENEID") | 283 | select(txdb,·keys=keys,·columns=cols,·keytype="GENEID") |
| 284 | </code></pre> | 284 | </code></pre> |
| 285 | <pre><code>##·Error·in·select(txdb,·keys·=·keys,·columns·=·cols,·keytype·=·"GENEID"):·could·not·find·function·"select" | 285 | <pre><code>##·Error·in·select(txdb,·keys·=·keys,·columns·=·cols,·keytype·=·"GENEID"):·could·not·find·function·"select" |
| 286 | </code></pre> | 286 | </code></pre> |
| 287 | <p>\end{Solution} | 287 | <p>\end{Solution}Ej`</p> |
| 288 | <h3·id="methods-for-returning-granges-objects">Methods·for·returning·<code>GRanges</code>·objects</h3> | 288 | <h3·id="methods-for-returning-granges-objects">Methods·for·returning·<code>GRanges</code>·objects</h3> |
| 289 | <p>Retrieving·data·with·select·is·useful,·but·sometimes·it·is·more | 289 | <p>Retrieving·data·with·select·is·useful,·but·sometimes·it·is·more |
| 290 | convenient·to·extract·the·result·as·<code>GRanges</code>·objects.··This·is | 290 | convenient·to·extract·the·result·as·<code>GRanges</code>·objects.··This·is |
| 291 | often·the·case·when·you·are·doing·counting·or·specialized·overlap | 291 | often·the·case·when·you·are·doing·counting·or·specialized·overlap |
| 292 | operations·downstream.··For·these·use·cases·there·is·another·family·of | 292 | operations·downstream.··For·these·use·cases·there·is·another·family·of |
| 293 | methods·available.</p> | 293 | methods·available.</p> |
| 294 | <p>Perhaps·the·most·common·operations·for·a·<code>TxDb</code>·object | 294 | <p>Perhaps·the·most·common·operations·for·a·<code>TxDb</code>·object |
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| 363 | </code></pre> | 363 | </code></pre> |
| 364 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'PR'·not·found | 364 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'PR'·not·found |
| 365 | </code></pre> | 365 | </code></pre> |
| 366 | <p>The·<code>exons</code>·and·<code>cds</code>·functions·can·also·be·used | 366 | <p>The·<code>exons</code>·and·<code>cds</code>·functions·can·also·be·used |
| 367 | in·a·similar·fashion·to·retrive·genomic·coordinates·for·exons·and | 367 | in·a·similar·fashion·to·retrive·genomic·coordinates·for·exons·and |
| 368 | coding·sequences.</p> | 368 | coding·sequences.</p> |
| 369 | <p>\begin{Exercise}·Use·</code>exons<code>to·retrieve·all·the·exons·from·chromosome·15.·How·does·the·length·of·this·compare·to·the·value·returned·by</code>transcripts<code>?·\end{Exercise} | 369 | <p>\begin{Exercise}·Use·</code>exons<code>to·retrieve·all·the·exons·from·chromosome·15.·How·does·the·length·of·this·compare·to·the·value·returned·by</code>transcripts<code>?·\end{Exercise} |
| 370 | ` | 370 | `Ej\begin{Solution}</p> |
| 371 | <pre><code·class="language-r">EX·<-·exons(txdb) | 371 | <pre><code·class="language-r">EX·<-·exons(txdb) |
| 372 | </code></pre> | 372 | </code></pre> |
| 373 | <pre><code>##·Error·in·exons(txdb):·could·not·find·function·"exons" | 373 | <pre><code>##·Error·in·exons(txdb):·could·not·find·function·"exons" |
| 374 | </code></pre> | 374 | </code></pre> |
| 375 | <pre><code·class="language-r">EX[1:4] | 375 | <pre><code·class="language-r">EX[1:4] |
| 376 | </code></pre> | 376 | </code></pre> |
| 377 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found | 377 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found |
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| 380 | </code></pre> | 380 | </code></pre> |
| 381 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found | 381 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found |
| 382 | </code></pre> | 382 | </code></pre> |
| 383 | <pre><code·class="language-r">length(GR) | 383 | <pre><code·class="language-r">length(GR) |
| 384 | </code></pre> | 384 | </code></pre> |
| 385 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'GR'·not·found | 385 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'GR'·not·found |
| 386 | </code></pre> | 386 | </code></pre> |
| 387 | <p>\end{Solution} | 387 | <p>\end{Solution}Ej`</p> |
| 388 | <h3·id="working-with-grouped-features">Working·with·Grouped·Features</h3> | 388 | <h3·id="working-with-grouped-features">Working·with·Grouped·Features</h3> |
| 389 | <p>Often·one·is·interested·in·how·particular·genomic·features·relate·to | 389 | <p>Often·one·is·interested·in·how·particular·genomic·features·relate·to |
| 390 | each·other,·and·not·just·their·location.··For·example,·it·might·be·of | 390 | each·other,·and·not·just·their·location.··For·example,·it·might·be·of |
| 391 | interest·to·group·transcripts·by·gene·or·to·group·exons·by·transcript. | 391 | interest·to·group·transcripts·by·gene·or·to·group·exons·by·transcript. |
| 392 | Such·groupings·are·supported·by·the·<code>transcriptsBy</code>, | 392 | Such·groupings·are·supported·by·the·<code>transcriptsBy</code>, |
| 393 | <code>exonsBy</code>,·and·<code>cdsBy</code>·functions.</p> | 393 | <code>exonsBy</code>,·and·<code>cdsBy</code>·functions.</p> |
| 394 | <p>The·following·call·can·be·used·to·group·transcripts·by·genes:</p> | 394 | <p>The·following·call·can·be·used·to·group·transcripts·by·genes:</p> |
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| 451 | unique·identifier·for·all·features.··In·this·situation,·the·group | 451 | unique·identifier·for·all·features.··In·this·situation,·the·group |
| 452 | label·will·be·a·synthetic·ID·created·by·<code>GenomicFeatures</code>·to | 452 | label·will·be·a·synthetic·ID·created·by·<code>GenomicFeatures</code>·to |
| 453 | keep·the·relations·between·features·consistent·in·the·database·this | 453 | keep·the·relations·between·features·consistent·in·the·database·this |
| 454 | was·the·case·in·the·2nd·example.··Even·though·the·results·will | 454 | was·the·case·in·the·2nd·example.··Even·though·the·results·will |
| 455 | sometimes·have·to·come·back·to·you·as·synthetic·IDs,·you·can·still | 455 | sometimes·have·to·come·back·to·you·as·synthetic·IDs,·you·can·still |
| 456 | always·retrieve·the·original·IDs.</p> | 456 | always·retrieve·the·original·IDs.</p> |
| 457 | <p>\begin{Exercise}·Starting·with·the·tx_ids·that·are·the·names·of·the·GRList·object·we·just·made,·use·</code>select<code>to·retrieve·that·matching·transcript·names.··Remember·that·the·list·used·a</code>by<code>·argument·=·"tx",·so·the·list·is·grouped·by·transcript·IDs.·\end{Exercise} | 457 | <p>\begin{Exercise}·Starting·with·the·tx_ids·that·are·the·names·of·the·GRList·object·we·just·made,·use·</code>select<code>to·retrieve·that·matching·transcript·names.··Remember·that·the·list·used·a</code>by<code>·argument·=·"tx",·so·the·list·is·grouped·by·transcript·IDs.·\end{Exercise} |
| 458 | ` | 458 | `Ej\begin{Solution}</p> |
| 459 | <pre><code·class="language-r">GRList·<-·exonsBy(txdb,·by·=·"tx") | 459 | <pre><code·class="language-r">GRList·<-·exonsBy(txdb,·by·=·"tx") |
| 460 | </code></pre> | 460 | </code></pre> |
| 461 | <pre><code>##·Error·in·exonsBy(txdb,·by·=·"tx"):·could·not·find·function·"exonsBy" | 461 | <pre><code>##·Error·in·exonsBy(txdb,·by·=·"tx"):·could·not·find·function·"exonsBy" |
| 462 | </code></pre> | 462 | </code></pre> |
| 463 | <pre><code·class="language-r">tx_ids·<-·names(GRList) | 463 | <pre><code·class="language-r">tx_ids·<-·names(GRList) |
| 464 | </code></pre> | 464 | </code></pre> |
| 465 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'GRList'·not·found | 465 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'GRList'·not·found |
| 466 | </code></pre> | 466 | </code></pre> |
| 467 | <pre><code·class="language-r">head(select(txdb,·keys=tx_ids,·columns="TXNAME",·keytype="TXID")) | 467 | <pre><code·class="language-r">head(select(txdb,·keys=tx_ids,·columns="TXNAME",·keytype="TXID")) |
| 468 | </code></pre> | 468 | </code></pre> |
| 469 | <pre><code>##·Error·in·select(txdb,·keys·=·tx_ids,·columns·=·"TXNAME",·keytype·=·"TXID"):·could·not·find·function·"select" | 469 | <pre><code>##·Error·in·select(txdb,·keys·=·tx_ids,·columns·=·"TXNAME",·keytype·=·"TXID"):·could·not·find·function·"select" |
| 470 | </code></pre> | 470 | </code></pre> |
| 471 | <p>\end{Solution} | 471 | <p>\end{Solution}Ej`</p> |
| 472 | <p>Finally,·the·order·of·the·results·in·a·<code>GRangesList</code>·object·can | 472 | <p>Finally,·the·order·of·the·results·in·a·<code>GRangesList</code>·object·can |
| 473 | vary·with·the·way·in·which·things·were·grouped.·In·most·cases·the | 473 | vary·with·the·way·in·which·things·were·grouped.·In·most·cases·the |
| 474 | grouped·elements·of·the·<code>GRangesList</code>·object·will·be·listed·in | 474 | grouped·elements·of·the·<code>GRangesList</code>·object·will·be·listed·in |
| 475 | the·order·that·they·occurred·along·the·chromosome.··However,·when | 475 | the·order·that·they·occurred·along·the·chromosome.··However,·when |
| 476 | exons·or·CDS·parts·are·grouped·by·transcript,·they·will·instead·be | 476 | exons·or·CDS·parts·are·grouped·by·transcript,·they·will·instead·be |
| 477 | grouped·according·to·their·position·along·the·transcript·itself. | 477 | grouped·according·to·their·position·along·the·transcript·itself. |
| 478 | This·is·important·because·alternative·splicing·can·mean·that·the | 478 | This·is·important·because·alternative·splicing·can·mean·that·the |
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| 1 | *\x8**\x8**\x8**\x8**\x8**\x8*·M\x8Ma\x8ak\x8ki\x8in\x8ng\x8g·a\x8an\x8nd\x8d·U\x8Ut\x8ti\x8il\x8li\x8iz\x8zi\x8in\x8ng\x8g·T\x8Tx\x8xD\x8Db\x8b·O\x8Ob\x8bj\x8je\x8ec\x8ct\x8ts\x8s·*\x8**\x8**\x8**\x8**\x8**\x8* | 1 | *\x8**\x8**\x8**\x8**\x8**\x8*·M\x8Ma\x8ak\x8ki\x8in\x8ng\x8g·a\x8an\x8nd\x8d·U\x8Ut\x8ti\x8il\x8li\x8iz\x8zi\x8in\x8ng\x8g·T\x8Tx\x8xD\x8Db\x8b·O\x8Ob\x8bj\x8je\x8ec\x8ct\x8ts\x8s·*\x8**\x8**\x8**\x8**\x8**\x8* |
| 2 | *\x8**\x8**\x8**\x8**\x8*·M\x8Ma\x8ar\x8rc\x8c·C\x8Ca\x8ar\x8rl\x8ls\x8so\x8on\x8n,\x8,·P\x8Pa\x8at\x8tr\x8ri\x8ic\x8ck\x8k·A\x8Ab\x8bo\x8oy\x8yo\x8ou\x8un\x8n,\x8,·H\x8He\x8er\x8rv\x8v?\x8é·P\x8Pa\x8ag\x8g?\x8ès\x8s,\x8,·S\x8Se\x8et\x8th\x8h·F\x8Fa\x8al\x8lc\x8co\x8on\x8n,\x8,·M\x8Ma\x8ar\x8rt\x8ti\x8in\x8n·M\x8Mo\x8or\x8rg\x8ga\x8an\x8n | 2 | *\x8**\x8**\x8**\x8**\x8*·M\x8Ma\x8ar\x8rc\x8c·C\x8Ca\x8ar\x8rl\x8ls\x8so\x8on\x8n,\x8,·P\x8Pa\x8at\x8tr\x8ri\x8ic\x8ck\x8k·A\x8Ab\x8bo\x8oy\x8yo\x8ou\x8un\x8n,\x8,·H\x8He\x8er\x8rv\x8v?\x8é·P\x8Pa\x8ag\x8g?\x8ès\x8s,\x8,·S\x8Se\x8et\x8th\x8h·F\x8Fa\x8al\x8lc\x8co\x8on\x8n,\x8,·M\x8Ma\x8ar\x8rt\x8ti\x8in\x8n·M\x8Mo\x8or\x8rg\x8ga\x8an\x8n |
| 3 | *\x8**\x8**\x8**\x8**\x8* | 3 | *\x8**\x8**\x8**\x8**\x8* |
| 4 | *\x8**\x8**\x8**\x8*· | 4 | *\x8**\x8**\x8**\x8*·F.Fr.ri.id.da.ay.y,.,·J.Ju.un.ne.e·0.07.7,.,·2.20.02.24.4·*\x8**\x8**\x8**\x8* |
| 5 | *\x8**\x8**\x8**\x8**\x8*·I\x8In\x8nt\x8tr\x8ro\x8od\x8du\x8uc\x8ct\x8ti\x8io\x8on\x8n·*\x8**\x8**\x8**\x8**\x8* | 5 | *\x8**\x8**\x8**\x8**\x8*·I\x8In\x8nt\x8tr\x8ro\x8od\x8du\x8uc\x8ct\x8ti\x8io\x8on\x8n·*\x8**\x8**\x8**\x8**\x8* |
| 6 | The·GenomicFeatures·package·retrieves·and·manages·transcript-related·features | 6 | The·GenomicFeatures·package·retrieves·and·manages·transcript-related·features |
| 7 | from·the·UCSC·Genome·Bioinformatics\footnote{(_\x8h_\x8t_\x8t_\x8p_\x8s_\x8:_\x8/_\x8/_\x8g_\x8e_\x8n_\x8o_\x8m_\x8e_\x8._\x8u_\x8c_\x8s_\x8c_\x8._\x8e_\x8d_\x8u_\x8/_\x8)_\x8}·and | 7 | from·the·UCSC·Genome·Bioinformatics\footnote{(_\x8h_\x8t_\x8t_\x8p_\x8s_\x8:_\x8/_\x8/_\x8g_\x8e_\x8n_\x8o_\x8m_\x8e_\x8._\x8u_\x8c_\x8s_\x8c_\x8._\x8e_\x8d_\x8u_\x8/_\x8)_\x8}·and |
| 8 | BioMart\footnote{(_\x8h_\x8t_\x8t_\x8p_\x8:_\x8/_\x8/_\x8w_\x8w_\x8w_\x8._\x8b_\x8i_\x8o_\x8m_\x8a_\x8r_\x8t_\x8._\x8o_\x8r_\x8g_\x8/_\x8)_\x8}·data·resources.·The·package·is | 8 | BioMart\footnote{(_\x8h_\x8t_\x8t_\x8p_\x8:_\x8/_\x8/_\x8w_\x8w_\x8w_\x8._\x8b_\x8i_\x8o_\x8m_\x8a_\x8r_\x8t_\x8._\x8o_\x8r_\x8g_\x8/_\x8)_\x8}·data·resources.·The·package·is |
| 9 | useful·for·ChIP-chip,·ChIP-seq,·and·RNA-seq·analyses. | 9 | useful·for·ChIP-chip,·ChIP-seq,·and·RNA-seq·analyses. |
| 10 | suppressPackageStartupMessages(library('GenomicFeatures')) | 10 | suppressPackageStartupMessages(library('GenomicFeatures')) |
| 11 | ##·Error·in·library("GenomicFeatures"):·there·is·no·package·called | 11 | ##·Error·in·library("GenomicFeatures"):·there·is·no·package·called |
| Offset 67, 20 lines modified | Offset 67, 20 lines modified | ||
| 67 | would·be·consulted·when·you·call·the·various·retrieval·methods…·If·you·need·to | 67 | would·be·consulted·when·you·call·the·various·retrieval·methods…·If·you·need·to |
| 68 | reset·back·to·the·original·seqlevels·(i.e.·to·the·seqlevels·stored·in·the·db), | 68 | reset·back·to·the·original·seqlevels·(i.e.·to·the·seqlevels·stored·in·the·db), |
| 69 | then·set·the·seqlevels·to·seqlevels0(txdb). | 69 | then·set·the·seqlevels·to·seqlevels0(txdb). |
| 70 | seqlevels(txdb)·<-·seqlevels0(txdb) | 70 | seqlevels(txdb)·<-·seqlevels0(txdb) |
| 71 | ##·Error·in·seqlevels0(txdb):·could·not·find·function·"seqlevels0" | 71 | ##·Error·in·seqlevels0(txdb):·could·not·find·function·"seqlevels0" |
| 72 | \begin{Exercise}·Use | 72 | \begin{Exercise}·Use |
| 73 | seqlevels·to·set·only·chromsome·15·to·be·active.·BTW,·the·rest·of·this·vignette | 73 | seqlevels·to·set·only·chromsome·15·to·be·active.·BTW,·the·rest·of·this·vignette |
| 74 | will·assume·you·have·succeeded·at·this.·\end{Exercise}·` | 74 | will·assume·you·have·succeeded·at·this.·\end{Exercise}·`Ej\begin{Solution} |
| 75 | seqlevels(txdb)·<-·"chr15" | 75 | seqlevels(txdb)·<-·"chr15" |
| 76 | ##·Error:·object·'txdb'·not·found | 76 | ##·Error:·object·'txdb'·not·found |
| 77 | seqlevels(txdb) | 77 | seqlevels(txdb) |
| 78 | ##·Error·in·seqlevels(txdb):·could·not·find·function·"seqlevels" | 78 | ##·Error·in·seqlevels(txdb):·could·not·find·function·"seqlevels" |
| 79 | \end{Solution} | 79 | \end{Solution}Ej` |
| 80 | *\x8**\x8**\x8**\x8*·R\x8Re\x8et\x8tr\x8ri\x8ie\x8ev\x8vi\x8in\x8ng\x8g·d\x8da\x8at\x8ta\x8a·u\x8us\x8si\x8in\x8ng\x8g·t\x8th\x8he\x8e·s\x8se\x8el\x8le\x8ec\x8ct\x8t·m\x8me\x8et\x8th\x8ho\x8od\x8d·*\x8**\x8**\x8**\x8* | 80 | *\x8**\x8**\x8**\x8*·R\x8Re\x8et\x8tr\x8ri\x8ie\x8ev\x8vi\x8in\x8ng\x8g·d\x8da\x8at\x8ta\x8a·u\x8us\x8si\x8in\x8ng\x8g·t\x8th\x8he\x8e·s\x8se\x8el\x8le\x8ec\x8ct\x8t·m\x8me\x8et\x8th\x8ho\x8od\x8d·*\x8**\x8**\x8**\x8* |
| 81 | The·TxDb·objects·inherit·from·AnnotationDb·objects·(just·as·the·ChipDb·and | 81 | The·TxDb·objects·inherit·from·AnnotationDb·objects·(just·as·the·ChipDb·and |
| 82 | OrgDb·objects·do).·One·of·the·implications·of·this·relationship·is·that·these | 82 | OrgDb·objects·do).·One·of·the·implications·of·this·relationship·is·that·these |
| 83 | object·ought·to·be·used·in·similar·ways·to·each·other.·Therefore·we·have | 83 | object·ought·to·be·used·in·similar·ways·to·each·other.·Therefore·we·have |
| 84 | written·supporting·columns,·keytypes,·keys·and·select·methods·for·TxDb·objects. | 84 | written·supporting·columns,·keytypes,·keys·and·select·methods·for·TxDb·objects. |
| 85 | These·methods·can·be·a·useful·way·of·extracting·data·from·a·TxDb·object.·And | 85 | These·methods·can·be·a·useful·way·of·extracting·data·from·a·TxDb·object.·And |
| 86 | they·are·used·in·the·same·way·that·they·would·be·used·to·extract·information | 86 | they·are·used·in·the·same·way·that·they·would·be·used·to·extract·information |
| Offset 92, 22 lines modified | Offset 92, 22 lines modified | ||
| 92 | keytypes(txdb) | 92 | keytypes(txdb) |
| 93 | ##·Error·in·keytypes(txdb):·could·not·find·function·"keytypes" | 93 | ##·Error·in·keytypes(txdb):·could·not·find·function·"keytypes" |
| 94 | select(txdb,·keys·=·keys,·columns="TXNAME",·keytype="GENEID") | 94 | select(txdb,·keys·=·keys,·columns="TXNAME",·keytype="GENEID") |
| 95 | ##·Error·in·select(txdb,·keys·=·keys,·columns·=·"TXNAME",·keytype·=·"GENEID"): | 95 | ##·Error·in·select(txdb,·keys·=·keys,·columns·=·"TXNAME",·keytype·=·"GENEID"): |
| 96 | could·not·find·function·"select" | 96 | could·not·find·function·"select" |
| 97 | \begin{Exercise}·For·the·genes·in·the·example·above,·find·the·chromosome·and | 97 | \begin{Exercise}·For·the·genes·in·the·example·above,·find·the·chromosome·and |
| 98 | strand·information·that·will·go·with·each·of·the·transcript·names.·\end | 98 | strand·information·that·will·go·with·each·of·the·transcript·names.·\end |
| 99 | {Exercise}·` | 99 | {Exercise}·`Ej\begin{Solution} |
| 100 | columns(txdb) | 100 | columns(txdb) |
| 101 | ##·Error·in·columns(txdb):·could·not·find·function·"columns" | 101 | ##·Error·in·columns(txdb):·could·not·find·function·"columns" |
| 102 | cols·<-·c("TXNAME",·"TXSTRAND",·"TXCHROM") | 102 | cols·<-·c("TXNAME",·"TXSTRAND",·"TXCHROM") |
| 103 | select(txdb,·keys=keys,·columns=cols,·keytype="GENEID") | 103 | select(txdb,·keys=keys,·columns=cols,·keytype="GENEID") |
| 104 | ##·Error·in·select(txdb,·keys·=·keys,·columns·=·cols,·keytype·=·"GENEID"): | 104 | ##·Error·in·select(txdb,·keys·=·keys,·columns·=·cols,·keytype·=·"GENEID"): |
| 105 | could·not·find·function·"select" | 105 | could·not·find·function·"select" |
| 106 | \end{Solution} | 106 | \end{Solution}Ej` |
| 107 | *\x8**\x8**\x8**\x8*·M\x8Me\x8et\x8th\x8ho\x8od\x8ds\x8s·f\x8fo\x8or\x8r·r\x8re\x8et\x8tu\x8ur\x8rn\x8ni\x8in\x8ng\x8g·G\x8GR\x8Ra\x8an\x8ng\x8ge\x8es\x8s·o\x8ob\x8bj\x8je\x8ec\x8ct\x8ts\x8s·*\x8**\x8**\x8**\x8* | 107 | *\x8**\x8**\x8**\x8*·M\x8Me\x8et\x8th\x8ho\x8od\x8ds\x8s·f\x8fo\x8or\x8r·r\x8re\x8et\x8tu\x8ur\x8rn\x8ni\x8in\x8ng\x8g·G\x8GR\x8Ra\x8an\x8ng\x8ge\x8es\x8s·o\x8ob\x8bj\x8je\x8ec\x8ct\x8ts\x8s·*\x8**\x8**\x8**\x8* |
| 108 | Retrieving·data·with·select·is·useful,·but·sometimes·it·is·more·convenient·to | 108 | Retrieving·data·with·select·is·useful,·but·sometimes·it·is·more·convenient·to |
| 109 | extract·the·result·as·GRanges·objects.·This·is·often·the·case·when·you·are | 109 | extract·the·result·as·GRanges·objects.·This·is·often·the·case·when·you·are |
| 110 | doing·counting·or·specialized·overlap·operations·downstream.·For·these·use | 110 | doing·counting·or·specialized·overlap·operations·downstream.·For·these·use |
| 111 | cases·there·is·another·family·of·methods·available. | 111 | cases·there·is·another·family·of·methods·available. |
| 112 | Perhaps·the·most·common·operations·for·a·TxDb·object·is·to·retrieve·the·genomic | 112 | Perhaps·the·most·common·operations·for·a·TxDb·object·is·to·retrieve·the·genomic |
| 113 | coordinates·or·r\x8ra\x8an\x8ng\x8ge\x8es\x8s·for·exons,·transcripts·or·coding·sequences.·The·functions | 113 | coordinates·or·r\x8ra\x8an\x8ng\x8ge\x8es\x8s·for·exons,·transcripts·or·coding·sequences.·The·functions |
| Offset 154, 24 lines modified | Offset 154, 24 lines modified | ||
| 154 | function·"promoters" | 154 | function·"promoters" |
| 155 | PR | 155 | PR |
| 156 | ##·Error·in·eval(expr,·envir,·enclos):·object·'PR'·not·found | 156 | ##·Error·in·eval(expr,·envir,·enclos):·object·'PR'·not·found |
| 157 | The·exons·and·cds·functions·can·also·be·used·in·a·similar·fashion·to·retrive | 157 | The·exons·and·cds·functions·can·also·be·used·in·a·similar·fashion·to·retrive |
| 158 | genomic·coordinates·for·exons·and·coding·sequences. | 158 | genomic·coordinates·for·exons·and·coding·sequences. |
| 159 | \begin{Exercise}·Use | 159 | \begin{Exercise}·Use |
| 160 | exonsto·retrieve·all·the·exons·from·chromosome·15.·How·does·the·length·of·this | 160 | exonsto·retrieve·all·the·exons·from·chromosome·15.·How·does·the·length·of·this |
| 161 | compare·to·the·value·returned·bytranscripts?·\end{Exercise}·` | 161 | compare·to·the·value·returned·bytranscripts?·\end{Exercise}·`Ej\begin{Solution} |
| 162 | EX·<-·exons(txdb) | 162 | EX·<-·exons(txdb) |
| 163 | ##·Error·in·exons(txdb):·could·not·find·function·"exons" | 163 | ##·Error·in·exons(txdb):·could·not·find·function·"exons" |
| 164 | EX[1:4] | 164 | EX[1:4] |
| 165 | ##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found | 165 | ##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found |
| 166 | length(EX) | 166 | length(EX) |
| 167 | ##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found | 167 | ##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found |
| 168 | length(GR) | 168 | length(GR) |
| 169 | ##·Error·in·eval(expr,·envir,·enclos):·object·'GR'·not·found | 169 | ##·Error·in·eval(expr,·envir,·enclos):·object·'GR'·not·found |
| 170 | \end{Solution} | 170 | \end{Solution}Ej` |
| 171 | *\x8**\x8**\x8**\x8*·W\x8Wo\x8or\x8rk\x8ki\x8in\x8ng\x8g·w\x8wi\x8it\x8th\x8h·G\x8Gr\x8ro\x8ou\x8up\x8pe\x8ed\x8d·F\x8Fe\x8ea\x8at\x8tu\x8ur\x8re\x8es\x8s·*\x8**\x8**\x8**\x8* | 171 | *\x8**\x8**\x8**\x8*·W\x8Wo\x8or\x8rk\x8ki\x8in\x8ng\x8g·w\x8wi\x8it\x8th\x8h·G\x8Gr\x8ro\x8ou\x8up\x8pe\x8ed\x8d·F\x8Fe\x8ea\x8at\x8tu\x8ur\x8re\x8es\x8s·*\x8**\x8**\x8**\x8* |
| 172 | Often·one·is·interested·in·how·particular·genomic·features·relate·to·each | 172 | Often·one·is·interested·in·how·particular·genomic·features·relate·to·each |
| 173 | other,·and·not·just·their·location.·For·example,·it·might·be·of·interest·to | 173 | other,·and·not·just·their·location.·For·example,·it·might·be·of·interest·to |
| 174 | group·transcripts·by·gene·or·to·group·exons·by·transcript.·Such·groupings·are | 174 | group·transcripts·by·gene·or·to·group·exons·by·transcript.·Such·groupings·are |
| 175 | supported·by·the·transcriptsBy,·exonsBy,·and·cdsBy·functions. | 175 | supported·by·the·transcriptsBy,·exonsBy,·and·cdsBy·functions. |
| 176 | The·following·call·can·be·used·to·group·transcripts·by·genes: | 176 | The·following·call·can·be·used·to·group·transcripts·by·genes: |
| 177 | GRList·<-·transcriptsBy(txdb,·by·=·"gene") | 177 | GRList·<-·transcriptsBy(txdb,·by·=·"gene") |
| Offset 215, 23 lines modified | Offset 215, 23 lines modified | ||
| 215 | relations·between·features·consistent·in·the·database·this·was·the·case·in·the | 215 | relations·between·features·consistent·in·the·database·this·was·the·case·in·the |
| 216 | 2nd·example.·Even·though·the·results·will·sometimes·have·to·come·back·to·you·as | 216 | 2nd·example.·Even·though·the·results·will·sometimes·have·to·come·back·to·you·as |
| 217 | synthetic·IDs,·you·can·still·always·retrieve·the·original·IDs. | 217 | synthetic·IDs,·you·can·still·always·retrieve·the·original·IDs. |
| 218 | \begin{Exercise}·Starting·with·the·tx_ids·that·are·the·names·of·the·GRList | 218 | \begin{Exercise}·Starting·with·the·tx_ids·that·are·the·names·of·the·GRList |
| 219 | object·we·just·made,·use | 219 | object·we·just·made,·use |
| 220 | selectto·retrieve·that·matching·transcript·names.·Remember·that·the·list·used | 220 | selectto·retrieve·that·matching·transcript·names.·Remember·that·the·list·used |
| 221 | aby·argument·=·"tx",·so·the·list·is·grouped·by·transcript·IDs.·\end{Exercise} | 221 | aby·argument·=·"tx",·so·the·list·is·grouped·by·transcript·IDs.·\end{Exercise} |
| 222 | ` | 222 | `Ej\begin{Solution} |
| 223 | GRList·<-·exonsBy(txdb,·by·=·"tx") | 223 | GRList·<-·exonsBy(txdb,·by·=·"tx") |
| 224 | ##·Error·in·exonsBy(txdb,·by·=·"tx"):·could·not·find·function·"exonsBy" | 224 | ##·Error·in·exonsBy(txdb,·by·=·"tx"):·could·not·find·function·"exonsBy" |
| 225 | tx_ids·<-·names(GRList) | 225 | tx_ids·<-·names(GRList) |
| 226 | ##·Error·in·eval(expr,·envir,·enclos):·object·'GRList'·not·found | 226 | ##·Error·in·eval(expr,·envir,·enclos):·object·'GRList'·not·found |
| 227 | head(select(txdb,·keys=tx_ids,·columns="TXNAME",·keytype="TXID")) | 227 | head(select(txdb,·keys=tx_ids,·columns="TXNAME",·keytype="TXID")) |
| 228 | ##·Error·in·select(txdb,·keys·=·tx_ids,·columns·=·"TXNAME",·keytype·=·"TXID"): | 228 | ##·Error·in·select(txdb,·keys·=·tx_ids,·columns·=·"TXNAME",·keytype·=·"TXID"): |
| 229 | could·not·find·function·"select" | 229 | could·not·find·function·"select" |
| 230 | \end{Solution} | 230 | \end{Solution}Ej` |
| 231 | Finally,·the·order·of·the·results·in·a·GRangesList·object·can·vary·with·the·way | 231 | Finally,·the·order·of·the·results·in·a·GRangesList·object·can·vary·with·the·way |
| 232 | in·which·things·were·grouped.·In·most·cases·the·grouped·elements·of·the | 232 | in·which·things·were·grouped.·In·most·cases·the·grouped·elements·of·the |
| 233 | GRangesList·object·will·be·listed·in·the·order·that·they·occurred·along·the | 233 | GRangesList·object·will·be·listed·in·the·order·that·they·occurred·along·the |
| 234 | chromosome.·However,·when·exons·or·CDS·parts·are·grouped·by·transcript,·they | 234 | chromosome.·However,·when·exons·or·CDS·parts·are·grouped·by·transcript,·they |
| 235 | will·instead·be·grouped·according·to·their·position·along·the·transcript | 235 | will·instead·be·grouped·according·to·their·position·along·the·transcript |
| 236 | itself.·This·is·important·because·alternative·splicing·can·mean·that·the·order | 236 | itself.·This·is·important·because·alternative·splicing·can·mean·that·the·order |
| 237 | along·the·transcript·can·be·different·from·that·along·the·chromosome. | 237 | along·the·transcript·can·be·different·from·that·along·the·chromosome. |
| Offset 266, 22 lines modified | Offset 266, 22 lines modified | ||
| 266 | suppressWarnings(translate(tx_seqs1)) | 266 | suppressWarnings(translate(tx_seqs1)) |
| 267 | ##·Error·in·translate(tx_seqs1):·could·not·find·function·"translate" | 267 | ##·Error·in·translate(tx_seqs1):·could·not·find·function·"translate" |
| 268 | \begin{Exercise}·But·of·course·this·is·not·a·meaningful·translation,·because | 268 | \begin{Exercise}·But·of·course·this·is·not·a·meaningful·translation,·because |
| 269 | the·call·to | 269 | the·call·to |
| 270 | extractTranscriptSeqswill·have·extracted·all·the·transcribed·regions·of·the | 270 | extractTranscriptSeqswill·have·extracted·all·the·transcribed·regions·of·the |
| 271 | genome·regardless·of·whether·or·not·they·are·translated.·Look·at·the·manual | 271 | genome·regardless·of·whether·or·not·they·are·translated.·Look·at·the·manual |
| 272 | page·forextractTranscriptSeqs·and·see·how·you·can·use·cdsBy·to·only·translate | 272 | page·forextractTranscriptSeqs·and·see·how·you·can·use·cdsBy·to·only·translate |
| 273 | only·the·coding·regions.·\end{Exercise}·` | 273 | only·the·coding·regions.·\end{Exercise}·`Ej\begin{Solution} |
| 274 | cds_seqs·<-·extractTranscriptSeqs(Hsapiens, | 274 | cds_seqs·<-·extractTranscriptSeqs(Hsapiens, |
| 275 | ··································cdsBy(txdb,·by="tx",·use.names=TRUE)) | 275 | ··································cdsBy(txdb,·by="tx",·use.names=TRUE)) |
| 276 | ##·Error·in·extractTranscriptSeqs(Hsapiens,·cdsBy(txdb,·by·=·"tx",·use.names·= | 276 | ##·Error·in·extractTranscriptSeqs(Hsapiens,·cdsBy(txdb,·by·=·"tx",·use.names·= |
| 277 | TRUE)):·could·not·find·function·"extractTranscriptSeqs" | 277 | TRUE)):·could·not·find·function·"extractTranscriptSeqs" |
| 278 | translate(cds_seqs) | 278 | translate(cds_seqs) |
| 279 | ##·Error·in·translate(cds_seqs):·could·not·find·function·"translate" | 279 | ##·Error·in·translate(cds_seqs):·could·not·find·function·"translate" |
| 280 | \end{Solution} | 280 | \end{Solution}Ej` |
| 281 | *\x8**\x8**\x8**\x8**\x8*·C\x8Cr\x8re\x8ea\x8at\x8ti\x8in\x8ng\x8g·N\x8Ne\x8ew\x8w·T\x8Tx\x8xD\x8Db\x8b·O\x8Ob\x8bj\x8je\x8ec\x8ct\x8ts\x8s·o\x8or\x8r·P\x8Pa\x8ac\x8ck\x8ka\x8ag\x8ge\x8es\x8s·*\x8**\x8**\x8**\x8**\x8* | 281 | *\x8**\x8**\x8**\x8**\x8*·C\x8Cr\x8re\x8ea\x8at\x8ti\x8in\x8ng\x8g·N\x8Ne\x8ew\x8w·T\x8Tx\x8xD\x8Db\x8b·O\x8Ob\x8bj\x8je\x8ec\x8ct\x8ts\x8s·o\x8or\x8r·P\x8Pa\x8ac\x8ck\x8ka\x8ag\x8ge\x8es\x8s·*\x8**\x8**\x8**\x8**\x8* |
| 282 | The·GenomicFeatures·package·provides·functions·to·create·TxDb·objects·based·on | 282 | The·GenomicFeatures·package·provides·functions·to·create·TxDb·objects·based·on |
| 283 | data·downloaded·from·UCSC·Genome·Bioinformatics·or·BioMart.·The·following | 283 | data·downloaded·from·UCSC·Genome·Bioinformatics·or·BioMart.·The·following |
| 284 | subsections·demonstrate·the·use·of·these·functions.·There·is·also·support·for | 284 | subsections·demonstrate·the·use·of·these·functions.·There·is·also·support·for |
| 285 | creating·TxDb·objects·from·custom·data·sources·using·makeTxDb;·see·the·help | 285 | creating·TxDb·objects·from·custom·data·sources·using·makeTxDb;·see·the·help |
| 286 | page·for·this·function·for·details. | 286 | page·for·this·function·for·details. |
| 287 | *\x8**\x8**\x8**\x8*·U\x8Us\x8si\x8in\x8ng\x8g·m\x8ma\x8ak\x8ke\x8eT\x8Tx\x8xD\x8Db\x8bF\x8Fr\x8ro\x8om\x8mU\x8UC\x8CS\x8SC\x8C·*\x8**\x8**\x8**\x8* | 287 | *\x8**\x8**\x8**\x8*·U\x8Us\x8si\x8in\x8ng\x8g·m\x8ma\x8ak\x8ke\x8eT\x8Tx\x8xD\x8Db\x8bF\x8Fr\x8ro\x8om\x8mU\x8UC\x8CS\x8SC\x8C·*\x8**\x8**\x8**\x8* |
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| 1 | --- | 1 | --- |
| 2 | title:·"Making·and·Utilizing·TxDb·Objects" | 2 | title:·"Making·and·Utilizing·TxDb·Objects" |
| 3 | author:·"Marc·Carlson,·Patrick·Aboyoun,·Hervé·Pagès,·Seth·Falcon,·Martin·Morgan" | 3 | author:·"Marc·Carlson,·Patrick·Aboyoun,·Hervé·Pagès,·Seth·Falcon,·Martin·Morgan" |
| 4 | date:·" | 4 | date:·"Friday,·June·07,·2024" |
| 5 | package:·GenomicFeatures | 5 | package:·GenomicFeatures |
| 6 | output: | 6 | output: |
| 7 | ··BiocStyle::html_document: | 7 | ··BiocStyle::html_document: |
| 8 | ····df_print:·paged | 8 | ····df_print:·paged |
| 9 | ····toc_float:·true | 9 | ····toc_float:·true |
| 10 | vignette:·> | 10 | vignette:·> |
| 11 | ··%\VignetteIndexEntry{Making·and·Utilizing·TxDb·Objects} | 11 | ··%\VignetteIndexEntry{Making·and·Utilizing·TxDb·Objects} |
| Offset 818, 15 lines modified | Offset 818, 15 lines modified | ||
| 818 | ##·Matrix·products:·default | 818 | ##·Matrix·products:·default |
| 819 | ##·BLAS:···/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0· | 819 | ##·BLAS:···/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0· |
| 820 | ##·LAPACK:·/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 | 820 | ##·LAPACK:·/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 |
| 821 | ##· | 821 | ##· |
| 822 | ##·locale: | 822 | ##·locale: |
| 823 | ##·[1]·C | 823 | ##·[1]·C |
| 824 | ##· | 824 | ##· |
| 825 | ##·time·zone:·/usr/share/zoneinfo/Etc/GMT | 825 | ##·time·zone:·/usr/share/zoneinfo/Etc/GMT-14 |
| 826 | ##·tzcode·source:·system·(glibc) | 826 | ##·tzcode·source:·system·(glibc) |
| 827 | ##· | 827 | ##· |
| 828 | ##·attached·base·packages: | 828 | ##·attached·base·packages: |
| 829 | ##·[1]·stats·····graphics··grDevices·utils·····datasets··methods···base····· | 829 | ##·[1]·stats·····graphics··grDevices·utils·····datasets··methods···base····· |
| 830 | ##· | 830 | ##· |
| 831 | ##·other·attached·packages: | 831 | ##·other·attached·packages: |
| 832 | ##·[1]·markdown_1.12·knitr_1.46··· | 832 | ##·[1]·markdown_1.12·knitr_1.46··· |