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| 92 | <div·class="include-before"> | 92 | <div·class="include-before"> |
| 93 | </div> | 93 | </div> |
| 94 | <div·class="frontmatter"> | 94 | <div·class="frontmatter"> |
| 95 | <div·class="title"><h1>Making·and·Utilizing·TxDb·Objects</h1></div> | 95 | <div·class="title"><h1>Making·and·Utilizing·TxDb·Objects</h1></div> |
| 96 | <div·class="author"><h2>Marc·Carlson,·Patrick·Aboyoun,·Hervé·Pagès,·Seth·Falcon,·Martin·Morgan</h2></div> | 96 | <div·class="author"><h2>Marc·Carlson,·Patrick·Aboyoun,·Hervé·Pagès,·Seth·Falcon,·Martin·Morgan</h2></div> |
| 97 | <div·class="date"><h3> | 97 | <div·class="date"><h3>Sunday,·January·21,·2024</h3></div> |
| 98 | </div> | 98 | </div> |
| 99 | <div·class="body"> | 99 | <div·class="body"> |
| 100 | <h2>Introduction</h2> | 100 | <h2>Introduction</h2> |
| 101 | <p>The·<code>GenomicFeatures</code>·package·retrieves·and·manages | 101 | <p>The·<code>GenomicFeatures</code>·package·retrieves·and·manages |
| 102 | transcript-related·features·from·the·UCSC·Genome | 102 | transcript-related·features·from·the·UCSC·Genome |
| 103 | Bioinformatics\footnote{(<a·href="http://genome.ucsc.edu/)%7D">http://genome.ucsc.edu/)}</a>·and | 103 | Bioinformatics\footnote{(<a·href="http://genome.ucsc.edu/)%7D">http://genome.ucsc.edu/)}</a>·and |
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| 188 | to·the·seqlevels·stored·in·the·db),·then·set·the·seqlevels·to | 188 | to·the·seqlevels·stored·in·the·db),·then·set·the·seqlevels·to |
| 189 | <code>seqlevels0(txdb)</code>.</p> | 189 | <code>seqlevels0(txdb)</code>.</p> |
| 190 | <pre><code·class="language-r">seqlevels(txdb)·<-·seqlevels0(txdb) | 190 | <pre><code·class="language-r">seqlevels(txdb)·<-·seqlevels0(txdb) |
| 191 | </code></pre> | 191 | </code></pre> |
| 192 | <pre><code>##·Error·in·seqlevels0(txdb):·could·not·find·function·"seqlevels0" | 192 | <pre><code>##·Error·in·seqlevels0(txdb):·could·not·find·function·"seqlevels0" |
| 193 | </code></pre> | 193 | </code></pre> |
| 194 | <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} | 194 | <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} |
| 195 | ` | 195 | `Dw\begin{Solution}</p> |
| 196 | <pre><code·class="language-r">seqlevels(txdb)·<-·"chr15" | 196 | <pre><code·class="language-r">seqlevels(txdb)·<-·"chr15" |
| 197 | </code></pre> | 197 | </code></pre> |
| 198 | <pre><code>##·Error·in·seqlevels(txdb)·<-·"chr15":·object·'txdb'·not·found | 198 | <pre><code>##·Error·in·seqlevels(txdb)·<-·"chr15":·object·'txdb'·not·found |
| 199 | </code></pre> | 199 | </code></pre> |
| 200 | <pre><code·class="language-r">seqlevels(txdb) | 200 | <pre><code·class="language-r">seqlevels(txdb) |
| 201 | </code></pre> | 201 | </code></pre> |
| 202 | <pre><code>##·Error·in·seqlevels(txdb):·could·not·find·function·"seqlevels" | 202 | <pre><code>##·Error·in·seqlevels(txdb):·could·not·find·function·"seqlevels" |
| 203 | </code></pre> | 203 | </code></pre> |
| 204 | <p>\end{Solution} | 204 | <p>\end{Solution}Dw`</p> |
| 205 | <h3>Retrieving·data·using·the·select·method</h3> | 205 | <h3>Retrieving·data·using·the·select·method</h3> |
| 206 | <p>The·<code>TxDb</code>·objects·inherit·from·<code>AnnotationDb</code> | 206 | <p>The·<code>TxDb</code>·objects·inherit·from·<code>AnnotationDb</code> |
| 207 | objects·(just·as·the·<code>ChipDb</code>·and·<code>OrgDb</code>·objects·do). | 207 | objects·(just·as·the·<code>ChipDb</code>·and·<code>OrgDb</code>·objects·do). |
| 208 | One·of·the·implications·of·this·relationship·is·that·these·object | 208 | One·of·the·implications·of·this·relationship·is·that·these·object |
| 209 | ought·to·be·used·in·similar·ways·to·each·other.··Therefore·we·have | 209 | ought·to·be·used·in·similar·ways·to·each·other.··Therefore·we·have |
| 210 | written·supporting·<code>columns</code>,·<code>keytypes</code>,·<code>keys</code> | 210 | written·supporting·<code>columns</code>,·<code>keytypes</code>,·<code>keys</code> |
| 211 | and·<code>select</code>·methods·for·<code>TxDb</code>·objects.</p> | 211 | and·<code>select</code>·methods·for·<code>TxDb</code>·objects.</p> |
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| 224 | <pre><code>##·Error·in·keytypes(txdb):·could·not·find·function·"keytypes" | 224 | <pre><code>##·Error·in·keytypes(txdb):·could·not·find·function·"keytypes" |
| 225 | </code></pre> | 225 | </code></pre> |
| 226 | <pre><code·class="language-r">select(txdb,·keys·=·keys,·columns="TXNAME",·keytype="GENEID") | 226 | <pre><code·class="language-r">select(txdb,·keys·=·keys,·columns="TXNAME",·keytype="GENEID") |
| 227 | </code></pre> | 227 | </code></pre> |
| 228 | <pre><code>##·Error·in·select(txdb,·keys·=·keys,·columns·=·"TXNAME",·keytype·=·"GENEID"):·could·not·find·function·"select" | 228 | <pre><code>##·Error·in·select(txdb,·keys·=·keys,·columns·=·"TXNAME",·keytype·=·"GENEID"):·could·not·find·function·"select" |
| 229 | </code></pre> | 229 | </code></pre> |
| 230 | <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} | 230 | <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} |
| 231 | ` | 231 | `Dw\begin{Solution}</p> |
| 232 | <pre><code·class="language-r">columns(txdb) | 232 | <pre><code·class="language-r">columns(txdb) |
| 233 | </code></pre> | 233 | </code></pre> |
| 234 | <pre><code>##·Error·in·columns(txdb):·could·not·find·function·"columns" | 234 | <pre><code>##·Error·in·columns(txdb):·could·not·find·function·"columns" |
| 235 | </code></pre> | 235 | </code></pre> |
| 236 | <pre><code·class="language-r">cols·<-·c("TXNAME",·"TXSTRAND",·"TXCHROM") | 236 | <pre><code·class="language-r">cols·<-·c("TXNAME",·"TXSTRAND",·"TXCHROM") |
| 237 | select(txdb,·keys=keys,·columns=cols,·keytype="GENEID") | 237 | select(txdb,·keys=keys,·columns=cols,·keytype="GENEID") |
| 238 | </code></pre> | 238 | </code></pre> |
| 239 | <pre><code>##·Error·in·select(txdb,·keys·=·keys,·columns·=·cols,·keytype·=·"GENEID"):·could·not·find·function·"select" | 239 | <pre><code>##·Error·in·select(txdb,·keys·=·keys,·columns·=·cols,·keytype·=·"GENEID"):·could·not·find·function·"select" |
| 240 | </code></pre> | 240 | </code></pre> |
| 241 | <p>\end{Solution} | 241 | <p>\end{Solution}Dw`</p> |
| 242 | <h3>Methods·for·returning·<code>GRanges</code>·objects</h3> | 242 | <h3>Methods·for·returning·<code>GRanges</code>·objects</h3> |
| 243 | <p>Retrieving·data·with·select·is·useful,·but·sometimes·it·is·more | 243 | <p>Retrieving·data·with·select·is·useful,·but·sometimes·it·is·more |
| 244 | convenient·to·extract·the·result·as·<code>GRanges</code>·objects.··This·is | 244 | convenient·to·extract·the·result·as·<code>GRanges</code>·objects.··This·is |
| 245 | often·the·case·when·you·are·doing·counting·or·specialized·overlap | 245 | often·the·case·when·you·are·doing·counting·or·specialized·overlap |
| 246 | operations·downstream.··For·these·use·cases·there·is·another·family·of | 246 | operations·downstream.··For·these·use·cases·there·is·another·family·of |
| 247 | methods·available.</p> | 247 | methods·available.</p> |
| 248 | <p>Perhaps·the·most·common·operations·for·a·<code>TxDb</code>·object | 248 | <p>Perhaps·the·most·common·operations·for·a·<code>TxDb</code>·object |
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| 317 | </code></pre> | 317 | </code></pre> |
| 318 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'PR'·not·found | 318 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'PR'·not·found |
| 319 | </code></pre> | 319 | </code></pre> |
| 320 | <p>The·<code>exons</code>·and·<code>cds</code>·functions·can·also·be·used | 320 | <p>The·<code>exons</code>·and·<code>cds</code>·functions·can·also·be·used |
| 321 | in·a·similar·fashion·to·retrive·genomic·coordinates·for·exons·and | 321 | in·a·similar·fashion·to·retrive·genomic·coordinates·for·exons·and |
| 322 | coding·sequences.</p> | 322 | coding·sequences.</p> |
| 323 | <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} | 323 | <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} |
| 324 | ` | 324 | `Dw\begin{Solution}</p> |
| 325 | <pre><code·class="language-r">EX·<-·exons(txdb) | 325 | <pre><code·class="language-r">EX·<-·exons(txdb) |
| 326 | </code></pre> | 326 | </code></pre> |
| 327 | <pre><code>##·Error·in·exons(txdb):·could·not·find·function·"exons" | 327 | <pre><code>##·Error·in·exons(txdb):·could·not·find·function·"exons" |
| 328 | </code></pre> | 328 | </code></pre> |
| 329 | <pre><code·class="language-r">EX[1:4] | 329 | <pre><code·class="language-r">EX[1:4] |
| 330 | </code></pre> | 330 | </code></pre> |
| 331 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found | 331 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found |
| Offset 334, 15 lines modified | Offset 334, 15 lines modified | ||
| 334 | </code></pre> | 334 | </code></pre> |
| 335 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found | 335 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found |
| 336 | </code></pre> | 336 | </code></pre> |
| 337 | <pre><code·class="language-r">length(GR) | 337 | <pre><code·class="language-r">length(GR) |
| 338 | </code></pre> | 338 | </code></pre> |
| 339 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'GR'·not·found | 339 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'GR'·not·found |
| 340 | </code></pre> | 340 | </code></pre> |
| 341 | <p>\end{Solution} | 341 | <p>\end{Solution}Dw`</p> |
| 342 | <h3>Working·with·Grouped·Features</h3> | 342 | <h3>Working·with·Grouped·Features</h3> |
| 343 | <p>Often·one·is·interested·in·how·particular·genomic·features·relate·to | 343 | <p>Often·one·is·interested·in·how·particular·genomic·features·relate·to |
| 344 | each·other,·and·not·just·their·location.··For·example,·it·might·be·of | 344 | each·other,·and·not·just·their·location.··For·example,·it·might·be·of |
| 345 | interest·to·group·transcripts·by·gene·or·to·group·exons·by·transcript. | 345 | interest·to·group·transcripts·by·gene·or·to·group·exons·by·transcript. |
| 346 | Such·groupings·are·supported·by·the·<code>transcriptsBy</code>, | 346 | Such·groupings·are·supported·by·the·<code>transcriptsBy</code>, |
| 347 | <code>exonsBy</code>,·and·<code>cdsBy</code>·functions.</p> | 347 | <code>exonsBy</code>,·and·<code>cdsBy</code>·functions.</p> |
| 348 | <p>The·following·call·can·be·used·to·group·transcripts·by·genes:</p> | 348 | <p>The·following·call·can·be·used·to·group·transcripts·by·genes:</p> |
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| 405 | unique·identifier·for·all·features.··In·this·situation,·the·group | 405 | unique·identifier·for·all·features.··In·this·situation,·the·group |
| 406 | label·will·be·a·synthetic·ID·created·by·<code>GenomicFeatures</code>·to | 406 | label·will·be·a·synthetic·ID·created·by·<code>GenomicFeatures</code>·to |
| 407 | keep·the·relations·between·features·consistent·in·the·database·this | 407 | keep·the·relations·between·features·consistent·in·the·database·this |
| 408 | was·the·case·in·the·2nd·example.··Even·though·the·results·will | 408 | was·the·case·in·the·2nd·example.··Even·though·the·results·will |
| 409 | sometimes·have·to·come·back·to·you·as·synthetic·IDs,·you·can·still | 409 | sometimes·have·to·come·back·to·you·as·synthetic·IDs,·you·can·still |
| 410 | always·retrieve·the·original·IDs.</p> | 410 | always·retrieve·the·original·IDs.</p> |
| 411 | <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} | 411 | <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} |
| 412 | ` | 412 | `Dw\begin{Solution}</p> |
| 413 | <pre><code·class="language-r">GRList·<-·exonsBy(txdb,·by·=·"tx") | 413 | <pre><code·class="language-r">GRList·<-·exonsBy(txdb,·by·=·"tx") |
| 414 | </code></pre> | 414 | </code></pre> |
| 415 | <pre><code>##·Error·in·exonsBy(txdb,·by·=·"tx"):·could·not·find·function·"exonsBy" | 415 | <pre><code>##·Error·in·exonsBy(txdb,·by·=·"tx"):·could·not·find·function·"exonsBy" |
| 416 | </code></pre> | 416 | </code></pre> |
| 417 | <pre><code·class="language-r">tx_ids·<-·names(GRList) | 417 | <pre><code·class="language-r">tx_ids·<-·names(GRList) |
| 418 | </code></pre> | 418 | </code></pre> |
| 419 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'GRList'·not·found | 419 | <pre><code>##·Error·in·eval(expr,·envir,·enclos):·object·'GRList'·not·found |
| 420 | </code></pre> | 420 | </code></pre> |
| 421 | <pre><code·class="language-r">head(select(txdb,·keys=tx_ids,·columns="TXNAME",·keytype="TXID")) | 421 | <pre><code·class="language-r">head(select(txdb,·keys=tx_ids,·columns="TXNAME",·keytype="TXID")) |
| 422 | </code></pre> | 422 | </code></pre> |
| 423 | <pre><code>##·Error·in·select(txdb,·keys·=·tx_ids,·columns·=·"TXNAME",·keytype·=·"TXID"):·could·not·find·function·"select" | 423 | <pre><code>##·Error·in·select(txdb,·keys·=·tx_ids,·columns·=·"TXNAME",·keytype·=·"TXID"):·could·not·find·function·"select" |
| 424 | </code></pre> | 424 | </code></pre> |
| 425 | <p>\end{Solution} | 425 | <p>\end{Solution}Dw`</p> |
| 426 | <p>Finally,·the·order·of·the·results·in·a·<code>GRangesList</code>·object·can | 426 | <p>Finally,·the·order·of·the·results·in·a·<code>GRangesList</code>·object·can |
| 427 | vary·with·the·way·in·which·things·were·grouped.·In·most·cases·the | 427 | vary·with·the·way·in·which·things·were·grouped.·In·most·cases·the |
| 428 | grouped·elements·of·the·<code>GRangesList</code>·object·will·be·listed·in | 428 | grouped·elements·of·the·<code>GRangesList</code>·object·will·be·listed·in |
| 429 | the·order·that·they·occurred·along·the·chromosome.··However,·when | 429 | the·order·that·they·occurred·along·the·chromosome.··However,·when |
| 430 | exons·or·CDS·are·grouped·by·transcript,·they·will·instead·be·grouped | 430 | exons·or·CDS·are·grouped·by·transcript,·they·will·instead·be·grouped |
| 431 | according·to·their·position·along·the·transcript·itself.··This·is | 431 | according·to·their·position·along·the·transcript·itself.··This·is |
| 432 | important·because·alternative·splicing·can·mean·that·the·order·along | 432 | important·because·alternative·splicing·can·mean·that·the·order·along |
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| 1 | ******·Making·and·Utilizing·TxDb·Objects·****** | 1 | ******·Making·and·Utilizing·TxDb·Objects·****** |
| 2 | *****·Marc·Carlson,·Patrick·Aboyoun,·Hervé·Pagès,·Seth·Falcon,·Martin·Morgan | 2 | *****·Marc·Carlson,·Patrick·Aboyoun,·Hervé·Pagès,·Seth·Falcon,·Martin·Morgan |
| 3 | ***** | 3 | ***** |
| 4 | ****· | 4 | ****·Sunday,·January·21,·2024·**** |
| 5 | *****·Introduction·***** | 5 | *****·Introduction·***** |
| 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{(http://genome.ucsc.edu/)}·and | 7 | from·the·UCSC·Genome·Bioinformatics\footnote{(http://genome.ucsc.edu/)}·and |
| 8 | BioMart\footnote{(http://www.biomart.org/)}·data·resources.·The·package·is | 8 | BioMart\footnote{(http://www.biomart.org/)}·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 69, 20 lines modified | Offset 69, 20 lines modified | ||
| 69 | would·be·consulted·when·you·call·the·various·retrieval·methods⦷If·you·need | 69 | would·be·consulted·when·you·call·the·various·retrieval·methods⦷If·you·need |
| 70 | to·reset·back·to·the·original·seqlevels·(i.e.·to·the·seqlevels·stored·in·the | 70 | to·reset·back·to·the·original·seqlevels·(i.e.·to·the·seqlevels·stored·in·the |
| 71 | db),·then·set·the·seqlevels·to·seqlevels0(txdb). | 71 | db),·then·set·the·seqlevels·to·seqlevels0(txdb). |
| 72 | seqlevels(txdb)·<-·seqlevels0(txdb) | 72 | seqlevels(txdb)·<-·seqlevels0(txdb) |
| 73 | ##·Error·in·seqlevels0(txdb):·could·not·find·function·"seqlevels0" | 73 | ##·Error·in·seqlevels0(txdb):·could·not·find·function·"seqlevels0" |
| 74 | \begin{Exercise}·Use | 74 | \begin{Exercise}·Use |
| 75 | seqlevelsto·set·only·chromsome·15·to·be·active.·BTW,·the·rest·of·this·vignette | 75 | seqlevelsto·set·only·chromsome·15·to·be·active.·BTW,·the·rest·of·this·vignette |
| 76 | will·assume·you·have·succeeded·at·this.·\end{Exercise}·` | 76 | will·assume·you·have·succeeded·at·this.·\end{Exercise}·`Dw\begin{Solution} |
| 77 | seqlevels(txdb)·<-·"chr15" | 77 | seqlevels(txdb)·<-·"chr15" |
| 78 | ##·Error·in·seqlevels(txdb)·<-·"chr15":·object·'txdb'·not·found | 78 | ##·Error·in·seqlevels(txdb)·<-·"chr15":·object·'txdb'·not·found |
| 79 | seqlevels(txdb) | 79 | seqlevels(txdb) |
| 80 | ##·Error·in·seqlevels(txdb):·could·not·find·function·"seqlevels" | 80 | ##·Error·in·seqlevels(txdb):·could·not·find·function·"seqlevels" |
| 81 | \end{Solution} | 81 | \end{Solution}Dw` |
| 82 | ****·Retrieving·data·using·the·select·method·**** | 82 | ****·Retrieving·data·using·the·select·method·**** |
| 83 | The·TxDb·objects·inherit·from·AnnotationDb·objects·(just·as·the·ChipDb·and | 83 | The·TxDb·objects·inherit·from·AnnotationDb·objects·(just·as·the·ChipDb·and |
| 84 | OrgDb·objects·do).·One·of·the·implications·of·this·relationship·is·that·these | 84 | OrgDb·objects·do).·One·of·the·implications·of·this·relationship·is·that·these |
| 85 | object·ought·to·be·used·in·similar·ways·to·each·other.·Therefore·we·have | 85 | object·ought·to·be·used·in·similar·ways·to·each·other.·Therefore·we·have |
| 86 | written·supporting·columns,·keytypes,·keys·and·select·methods·for·TxDb·objects. | 86 | written·supporting·columns,·keytypes,·keys·and·select·methods·for·TxDb·objects. |
| 87 | These·methods·can·be·a·useful·way·of·extracting·data·from·a·TxDb·object.·And | 87 | These·methods·can·be·a·useful·way·of·extracting·data·from·a·TxDb·object.·And |
| 88 | they·are·used·in·the·same·way·that·they·would·be·used·to·extract·information | 88 | they·are·used·in·the·same·way·that·they·would·be·used·to·extract·information |
| Offset 94, 22 lines modified | Offset 94, 22 lines modified | ||
| 94 | keytypes(txdb) | 94 | keytypes(txdb) |
| 95 | ##·Error·in·keytypes(txdb):·could·not·find·function·"keytypes" | 95 | ##·Error·in·keytypes(txdb):·could·not·find·function·"keytypes" |
| 96 | select(txdb,·keys·=·keys,·columns="TXNAME",·keytype="GENEID") | 96 | select(txdb,·keys·=·keys,·columns="TXNAME",·keytype="GENEID") |
| 97 | ##·Error·in·select(txdb,·keys·=·keys,·columns·=·"TXNAME",·keytype·=·"GENEID"): | 97 | ##·Error·in·select(txdb,·keys·=·keys,·columns·=·"TXNAME",·keytype·=·"GENEID"): |
| 98 | could·not·find·function·"select" | 98 | could·not·find·function·"select" |
| 99 | \begin{Exercise}·For·the·genes·in·the·example·above,·find·the·chromosome·and | 99 | \begin{Exercise}·For·the·genes·in·the·example·above,·find·the·chromosome·and |
| 100 | strand·information·that·will·go·with·each·of·the·transcript·names.·\end | 100 | strand·information·that·will·go·with·each·of·the·transcript·names.·\end |
| 101 | {Exercise}·` | 101 | {Exercise}·`Dw\begin{Solution} |
| 102 | columns(txdb) | 102 | columns(txdb) |
| 103 | ##·Error·in·columns(txdb):·could·not·find·function·"columns" | 103 | ##·Error·in·columns(txdb):·could·not·find·function·"columns" |
| 104 | cols·<-·c("TXNAME",·"TXSTRAND",·"TXCHROM") | 104 | cols·<-·c("TXNAME",·"TXSTRAND",·"TXCHROM") |
| 105 | select(txdb,·keys=keys,·columns=cols,·keytype="GENEID") | 105 | select(txdb,·keys=keys,·columns=cols,·keytype="GENEID") |
| 106 | ##·Error·in·select(txdb,·keys·=·keys,·columns·=·cols,·keytype·=·"GENEID"): | 106 | ##·Error·in·select(txdb,·keys·=·keys,·columns·=·cols,·keytype·=·"GENEID"): |
| 107 | could·not·find·function·"select" | 107 | could·not·find·function·"select" |
| 108 | \end{Solution} | 108 | \end{Solution}Dw` |
| 109 | ****·Methods·for·returning·GRanges·objects·**** | 109 | ****·Methods·for·returning·GRanges·objects·**** |
| 110 | Retrieving·data·with·select·is·useful,·but·sometimes·it·is·more·convenient·to | 110 | Retrieving·data·with·select·is·useful,·but·sometimes·it·is·more·convenient·to |
| 111 | extract·the·result·as·GRanges·objects.·This·is·often·the·case·when·you·are | 111 | extract·the·result·as·GRanges·objects.·This·is·often·the·case·when·you·are |
| 112 | doing·counting·or·specialized·overlap·operations·downstream.·For·these·use | 112 | doing·counting·or·specialized·overlap·operations·downstream.·For·these·use |
| 113 | cases·there·is·another·family·of·methods·available. | 113 | cases·there·is·another·family·of·methods·available. |
| 114 | Perhaps·the·most·common·operations·for·a·TxDb·object·is·to·retrieve·the·genomic | 114 | Perhaps·the·most·common·operations·for·a·TxDb·object·is·to·retrieve·the·genomic |
| 115 | coordinates·or·ranges·for·exons,·transcripts·or·coding·sequences.·The·functions | 115 | coordinates·or·ranges·for·exons,·transcripts·or·coding·sequences.·The·functions |
| Offset 156, 24 lines modified | Offset 156, 24 lines modified | ||
| 156 | function·"promoters" | 156 | function·"promoters" |
| 157 | PR | 157 | PR |
| 158 | ##·Error·in·eval(expr,·envir,·enclos):·object·'PR'·not·found | 158 | ##·Error·in·eval(expr,·envir,·enclos):·object·'PR'·not·found |
| 159 | The·exons·and·cds·functions·can·also·be·used·in·a·similar·fashion·to·retrive | 159 | The·exons·and·cds·functions·can·also·be·used·in·a·similar·fashion·to·retrive |
| 160 | genomic·coordinates·for·exons·and·coding·sequences. | 160 | genomic·coordinates·for·exons·and·coding·sequences. |
| 161 | \begin{Exercise}·Use | 161 | \begin{Exercise}·Use |
| 162 | exonsto·retrieve·all·the·exons·from·chromosome·15.·How·does·the·length·of·this | 162 | exonsto·retrieve·all·the·exons·from·chromosome·15.·How·does·the·length·of·this |
| 163 | compare·to·the·value·returned·bytranscripts?·\end{Exercise}·` | 163 | compare·to·the·value·returned·bytranscripts?·\end{Exercise}·`Dw\begin{Solution} |
| 164 | EX·<-·exons(txdb) | 164 | EX·<-·exons(txdb) |
| 165 | ##·Error·in·exons(txdb):·could·not·find·function·"exons" | 165 | ##·Error·in·exons(txdb):·could·not·find·function·"exons" |
| 166 | EX[1:4] | 166 | EX[1:4] |
| 167 | ##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found | 167 | ##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found |
| 168 | length(EX) | 168 | length(EX) |
| 169 | ##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found | 169 | ##·Error·in·eval(expr,·envir,·enclos):·object·'EX'·not·found |
| 170 | length(GR) | 170 | length(GR) |
| 171 | ##·Error·in·eval(expr,·envir,·enclos):·object·'GR'·not·found | 171 | ##·Error·in·eval(expr,·envir,·enclos):·object·'GR'·not·found |
| 172 | \end{Solution} | 172 | \end{Solution}Dw` |
| 173 | ****·Working·with·Grouped·Features·**** | 173 | ****·Working·with·Grouped·Features·**** |
| 174 | Often·one·is·interested·in·how·particular·genomic·features·relate·to·each | 174 | Often·one·is·interested·in·how·particular·genomic·features·relate·to·each |
| 175 | other,·and·not·just·their·location.·For·example,·it·might·be·of·interest·to | 175 | other,·and·not·just·their·location.·For·example,·it·might·be·of·interest·to |
| 176 | group·transcripts·by·gene·or·to·group·exons·by·transcript.·Such·groupings·are | 176 | group·transcripts·by·gene·or·to·group·exons·by·transcript.·Such·groupings·are |
| 177 | supported·by·the·transcriptsBy,·exonsBy,·and·cdsBy·functions. | 177 | supported·by·the·transcriptsBy,·exonsBy,·and·cdsBy·functions. |
| 178 | The·following·call·can·be·used·to·group·transcripts·by·genes: | 178 | The·following·call·can·be·used·to·group·transcripts·by·genes: |
| 179 | GRList·<-·transcriptsBy(txdb,·by·=·"gene") | 179 | GRList·<-·transcriptsBy(txdb,·by·=·"gene") |
| Offset 217, 23 lines modified | Offset 217, 23 lines modified | ||
| 217 | relations·between·features·consistent·in·the·database·this·was·the·case·in·the | 217 | relations·between·features·consistent·in·the·database·this·was·the·case·in·the |
| 218 | 2nd·example.·Even·though·the·results·will·sometimes·have·to·come·back·to·you·as | 218 | 2nd·example.·Even·though·the·results·will·sometimes·have·to·come·back·to·you·as |
| 219 | synthetic·IDs,·you·can·still·always·retrieve·the·original·IDs. | 219 | synthetic·IDs,·you·can·still·always·retrieve·the·original·IDs. |
| 220 | \begin{Exercise}·Starting·with·the·tx_ids·that·are·the·names·of·the·GRList | 220 | \begin{Exercise}·Starting·with·the·tx_ids·that·are·the·names·of·the·GRList |
| 221 | object·we·just·made,·use | 221 | object·we·just·made,·use |
| 222 | selectto·retrieve·that·matching·transcript·names.·Remember·that·the·list·used | 222 | selectto·retrieve·that·matching·transcript·names.·Remember·that·the·list·used |
| 223 | abyargument·=·"tx",·so·the·list·is·grouped·by·transcript·IDs.·\end{Exercise} | 223 | abyargument·=·"tx",·so·the·list·is·grouped·by·transcript·IDs.·\end{Exercise} |
| 224 | ` | 224 | `Dw\begin{Solution} |
| 225 | GRList·<-·exonsBy(txdb,·by·=·"tx") | 225 | GRList·<-·exonsBy(txdb,·by·=·"tx") |
| 226 | ##·Error·in·exonsBy(txdb,·by·=·"tx"):·could·not·find·function·"exonsBy" | 226 | ##·Error·in·exonsBy(txdb,·by·=·"tx"):·could·not·find·function·"exonsBy" |
| 227 | tx_ids·<-·names(GRList) | 227 | tx_ids·<-·names(GRList) |
| 228 | ##·Error·in·eval(expr,·envir,·enclos):·object·'GRList'·not·found | 228 | ##·Error·in·eval(expr,·envir,·enclos):·object·'GRList'·not·found |
| 229 | head(select(txdb,·keys=tx_ids,·columns="TXNAME",·keytype="TXID")) | 229 | head(select(txdb,·keys=tx_ids,·columns="TXNAME",·keytype="TXID")) |
| 230 | ##·Error·in·select(txdb,·keys·=·tx_ids,·columns·=·"TXNAME",·keytype·=·"TXID"): | 230 | ##·Error·in·select(txdb,·keys·=·tx_ids,·columns·=·"TXNAME",·keytype·=·"TXID"): |
| 231 | could·not·find·function·"select" | 231 | could·not·find·function·"select" |
| 232 | \end{Solution} | 232 | \end{Solution}Dw` |
| 233 | Finally,·the·order·of·the·results·in·a·GRangesList·object·can·vary·with·the·way | 233 | Finally,·the·order·of·the·results·in·a·GRangesList·object·can·vary·with·the·way |
| 234 | in·which·things·were·grouped.·In·most·cases·the·grouped·elements·of·the | 234 | in·which·things·were·grouped.·In·most·cases·the·grouped·elements·of·the |
| 235 | GRangesList·object·will·be·listed·in·the·order·that·they·occurred·along·the | 235 | GRangesList·object·will·be·listed·in·the·order·that·they·occurred·along·the |
| 236 | chromosome.·However,·when·exons·or·CDS·are·grouped·by·transcript,·they·will | 236 | chromosome.·However,·when·exons·or·CDS·are·grouped·by·transcript,·they·will |
| 237 | instead·be·grouped·according·to·their·position·along·the·transcript·itself. | 237 | instead·be·grouped·according·to·their·position·along·the·transcript·itself. |
| 238 | This·is·important·because·alternative·splicing·can·mean·that·the·order·along | 238 | This·is·important·because·alternative·splicing·can·mean·that·the·order·along |
| 239 | the·transcript·can·be·different·from·that·along·the·chromosome. | 239 | the·transcript·can·be·different·from·that·along·the·chromosome. |
| Offset 268, 22 lines modified | Offset 268, 22 lines modified | ||
| 268 | suppressWarnings(translate(tx_seqs1)) | 268 | suppressWarnings(translate(tx_seqs1)) |
| 269 | ##·Error·in·translate(tx_seqs1):·could·not·find·function·"translate" | 269 | ##·Error·in·translate(tx_seqs1):·could·not·find·function·"translate" |
| 270 | \begin{Exercise}·But·of·course·this·is·not·a·meaningful·translation,·because | 270 | \begin{Exercise}·But·of·course·this·is·not·a·meaningful·translation,·because |
| 271 | the·call·to | 271 | the·call·to |
| 272 | extractTranscriptSeqswill·have·extracted·all·the·transcribed·regions·of·the | 272 | extractTranscriptSeqswill·have·extracted·all·the·transcribed·regions·of·the |
| 273 | genome·regardless·of·whether·or·not·they·are·translated.·Look·at·the·manual | 273 | genome·regardless·of·whether·or·not·they·are·translated.·Look·at·the·manual |
| 274 | page·forextractTranscriptSeqsand·see·how·you·can·use·cdsBy·to·only·translate | 274 | page·forextractTranscriptSeqsand·see·how·you·can·use·cdsBy·to·only·translate |
| 275 | only·the·coding·regions.·\end{Exercise}·` | 275 | only·the·coding·regions.·\end{Exercise}·`Dw\begin{Solution} |
| 276 | cds_seqs·<-·extractTranscriptSeqs(Hsapiens, | 276 | cds_seqs·<-·extractTranscriptSeqs(Hsapiens, |
| 277 | ··································cdsBy(txdb,·by="tx",·use.names=TRUE)) | 277 | ··································cdsBy(txdb,·by="tx",·use.names=TRUE)) |
| 278 | ##·Error·in·extractTranscriptSeqs(Hsapiens,·cdsBy(txdb,·by·=·"tx",·use.names·= | 278 | ##·Error·in·extractTranscriptSeqs(Hsapiens,·cdsBy(txdb,·by·=·"tx",·use.names·= |
| 279 | TRUE)):·could·not·find·function·"extractTranscriptSeqs" | 279 | TRUE)):·could·not·find·function·"extractTranscriptSeqs" |
| 280 | translate(cds_seqs) | 280 | translate(cds_seqs) |
| 281 | ##·Error·in·translate(cds_seqs):·could·not·find·function·"translate" | 281 | ##·Error·in·translate(cds_seqs):·could·not·find·function·"translate" |
| 282 | \end{Solution} | 282 | \end{Solution}Dw` |
| 283 | *****·Creating·New·TxDb·Objects·or·Packages·***** | 283 | *****·Creating·New·TxDb·Objects·or·Packages·***** |
| 284 | The·GenomicFeatures·package·provides·functions·to·create·TxDb·objects·based·on | 284 | The·GenomicFeatures·package·provides·functions·to·create·TxDb·objects·based·on |
| 285 | data·downloaded·from·UCSC·Genome·Bioinformatics·or·BioMart.·The·following | 285 | data·downloaded·from·UCSC·Genome·Bioinformatics·or·BioMart.·The·following |
| 286 | subsections·demonstrate·the·use·of·these·functions.·There·is·also·support·for | 286 | subsections·demonstrate·the·use·of·these·functions.·There·is·also·support·for |
| 287 | creating·TxDb·objects·from·custom·data·sources·using·makeTxDb;·see·the·help | 287 | creating·TxDb·objects·from·custom·data·sources·using·makeTxDb;·see·the·help |
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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:·"Sunday,·January·21,·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} |