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| 142 | <div·class="frontmatter"> | 142 | <div·class="frontmatter"> |
| 143 | <div·class="title"><h1>Obtaining·and·Utilizing·TxDb·Objects</h1></div> | 143 | <div·class="title"><h1>Obtaining·and·Utilizing·TxDb·Objects</h1></div> |
| 144 | <div·class="author"><h2>list(name·=·“Marc·Carlson”) | 144 | <div·class="author"><h2>list(name·=·“Marc·Carlson”) |
| 145 | list(name·=·“Patrick·Aboyoun”) | 145 | list(name·=·“Patrick·Aboyoun”) |
| 146 | list(name·=·“Herv<U+00E9>·Pag<U+00E8>s”) | 146 | list(name·=·“Herv<U+00E9>·Pag<U+00E8>s”) |
| 147 | list(name·=·“Seth·Falcon”) | 147 | list(name·=·“Seth·Falcon”) |
| 148 | list(name·=·“Martin·Morgan”)</h2></div> | 148 | list(name·=·“Martin·Morgan”)</h2></div> |
| 149 | <div·class="date"><h3> | 149 | <div·class="date"><h3>Monday,·October·20,·2025</h3></div> |
| 150 | </div> | 150 | </div> |
| 151 | <div·class="body"> | 151 | <div·class="body"> |
| 152 | <h1·id="introduction">Introduction</h1> | 152 | <h1·id="introduction">Introduction</h1> |
| 153 | <p>The·<code>GenomicFeatures</code>·package·implements·the·<code>TxDb</code>·container·for | 153 | <p>The·<code>GenomicFeatures</code>·package·implements·the·<code>TxDb</code>·container·for |
| 154 | storing·transcript·metadata·for·a·given·organism.·A·<code>TxDb</code>·object | 154 | storing·transcript·metadata·for·a·given·organism.·A·<code>TxDb</code>·object |
| 155 | stores·the·genomic·positions·of·the·5’·and·3’·untranslated·regions | 155 | stores·the·genomic·positions·of·the·5’·and·3’·untranslated·regions |
| 156 | (UTRs),·protein·coding·sequences·(CDSs),·and·exons·for·a·set·of·mRNA | 156 | (UTRs),·protein·coding·sequences·(CDSs),·and·exons·for·a·set·of·mRNA |
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| 563 | ##·Matrix·products:·default | 563 | ##·Matrix·products:·default |
| 564 | ##·BLAS:···/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.1· | 564 | ##·BLAS:···/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.1· |
| 565 | ##·LAPACK:·/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1;··LAPACK·version·3.12.0 | 565 | ##·LAPACK:·/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1;··LAPACK·version·3.12.0 |
| 566 | ##· | 566 | ##· |
| 567 | ##·locale: | 567 | ##·locale: |
| 568 | ##·[1]·C | 568 | ##·[1]·C |
| 569 | ##· | 569 | ##· |
| 570 | ##·time·zone:·/usr/share/zoneinfo/Etc/GMT | 570 | ##·time·zone:·/usr/share/zoneinfo/Etc/GMT-14 |
| 571 | ##·tzcode·source:·system·(glibc) | 571 | ##·tzcode·source:·system·(glibc) |
| 572 | ##· | 572 | ##· |
| 573 | ##·attached·base·packages: | 573 | ##·attached·base·packages: |
| 574 | ##·[1]·stats·····graphics··grDevices·utils·····datasets··methods···base····· | 574 | ##·[1]·stats·····graphics··grDevices·utils·····datasets··methods···base····· |
| 575 | ##· | 575 | ##· |
| 576 | ##·other·attached·packages: | 576 | ##·other·attached·packages: |
| 577 | ##·[1]·markdown_1.13·knitr_1.50··· | 577 | ##·[1]·markdown_1.13·knitr_1.50··· |
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| 1 | ******·Obtaining·and·Utilizing·TxDb·Objects·****** | 1 | ******·Obtaining·and·Utilizing·TxDb·Objects·****** |
| 2 | *****·list(name·=·“Marc·Carlson”)·list(name·=·“Patrick·Aboyoun”)·list(name·= | 2 | *****·list(name·=·“Marc·Carlson”)·list(name·=·“Patrick·Aboyoun”)·list(name·= |
| 3 | “Herv<U+00E9>·Pag<U+00E8>s”)·list(name·=·“Seth·Falcon”)·list(name·=·“Martin | 3 | “Herv<U+00E9>·Pag<U+00E8>s”)·list(name·=·“Seth·Falcon”)·list(name·=·“Martin |
| 4 | Morgan”)·***** | 4 | Morgan”)·***** |
| 5 | ****· | 5 | ****·Monday,·October·20,·2025·**** |
| 6 | ******·Introduction·****** | 6 | ******·Introduction·****** |
| 7 | The·GenomicFeatures·package·implements·the·TxDb·container·for·storing | 7 | The·GenomicFeatures·package·implements·the·TxDb·container·for·storing |
| 8 | transcript·metadata·for·a·given·organism.·A·TxDb·object·stores·the·genomic | 8 | transcript·metadata·for·a·given·organism.·A·TxDb·object·stores·the·genomic |
| 9 | positions·of·the·5’·and·3’·untranslated·regions·(UTRs),·protein·coding | 9 | positions·of·the·5’·and·3’·untranslated·regions·(UTRs),·protein·coding |
| 10 | sequences·(CDSs),·and·exons·for·a·set·of·mRNA·transcripts.·The·genomic | 10 | sequences·(CDSs),·and·exons·for·a·set·of·mRNA·transcripts.·The·genomic |
| 11 | positions·are·stored·and·reported·with·respect·to·a·given·genome·assembly.·TxDb | 11 | positions·are·stored·and·reported·with·respect·to·a·given·genome·assembly.·TxDb |
| 12 | objects·have·numerous·accessors·functions·to·allow·such·features·to·be | 12 | objects·have·numerous·accessors·functions·to·allow·such·features·to·be |
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| 291 | ##·BLAS:···/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.1 | 291 | ##·BLAS:···/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.1 |
| 292 | ##·LAPACK:·/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1;··LAPACK | 292 | ##·LAPACK:·/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1;··LAPACK |
| 293 | version·3.12.0 | 293 | version·3.12.0 |
| 294 | ## | 294 | ## |
| 295 | ##·locale: | 295 | ##·locale: |
| 296 | ##·[1]·C | 296 | ##·[1]·C |
| 297 | ## | 297 | ## |
| 298 | ##·time·zone:·/usr/share/zoneinfo/Etc/GMT | 298 | ##·time·zone:·/usr/share/zoneinfo/Etc/GMT-14 |
| 299 | ##·tzcode·source:·system·(glibc) | 299 | ##·tzcode·source:·system·(glibc) |
| 300 | ## | 300 | ## |
| 301 | ##·attached·base·packages: | 301 | ##·attached·base·packages: |
| 302 | ##·[1]·stats·····graphics··grDevices·utils·····datasets··methods···base | 302 | ##·[1]·stats·····graphics··grDevices·utils·····datasets··methods···base |
| 303 | ## | 303 | ## |
| 304 | ##·other·attached·packages: | 304 | ##·other·attached·packages: |
| 305 | ##·[1]·markdown_1.13·knitr_1.50 | 305 | ##·[1]·markdown_1.13·knitr_1.50 |
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| 2 | title:·"Obtaining·and·Utilizing·TxDb·Objects" | 2 | title:·"Obtaining·and·Utilizing·TxDb·Objects" |
| 3 | author: | 3 | author: |
| 4 | -·name:·Marc·Carlson | 4 | -·name:·Marc·Carlson |
| 5 | -·name:·Patrick·Aboyoun | 5 | -·name:·Patrick·Aboyoun |
| 6 | -·name:·Hervé·Pagès | 6 | -·name:·Hervé·Pagès |
| 7 | -·name:·Seth·Falcon | 7 | -·name:·Seth·Falcon |
| 8 | -·name:·Martin·Morgan | 8 | -·name:·Martin·Morgan |
| 9 | date:·" | 9 | date:·"Monday,·October·20,·2025" |
| 10 | package:·GenomicFeatures | 10 | package:·GenomicFeatures |
| 11 | vignette:·| | 11 | vignette:·| |
| 12 | ··%\VignetteIndexEntry{Obtaining·and·Utilizing·TxDb·Objects} | 12 | ··%\VignetteIndexEntry{Obtaining·and·Utilizing·TxDb·Objects} |
| 13 | ··%\VignetteEngine{knitr::rmarkdown} | 13 | ··%\VignetteEngine{knitr::rmarkdown} |
| 14 | ··%\VignetteEncoding{UTF-8} | 14 | ··%\VignetteEncoding{UTF-8} |
| 15 | ··%\VignetteDepends{GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,BSgenome.Hsapiens.UCSC.hg19} | 15 | ··%\VignetteDepends{GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,BSgenome.Hsapiens.UCSC.hg19} |
| 16 | ··%\VignetteKeywords{annotation,·database} | 16 | ··%\VignetteKeywords{annotation,·database} |
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| 732 | ##·Matrix·products:·default | 732 | ##·Matrix·products:·default |
| 733 | ##·BLAS:···/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.1· | 733 | ##·BLAS:···/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.1· |
| 734 | ##·LAPACK:·/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1;··LAPACK·version·3.12.0 | 734 | ##·LAPACK:·/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1;··LAPACK·version·3.12.0 |
| 735 | ##· | 735 | ##· |
| 736 | ##·locale: | 736 | ##·locale: |
| 737 | ##·[1]·C | 737 | ##·[1]·C |
| 738 | ##· | 738 | ##· |
| 739 | ##·time·zone:·/usr/share/zoneinfo/Etc/GMT | 739 | ##·time·zone:·/usr/share/zoneinfo/Etc/GMT-14 |
| 740 | ##·tzcode·source:·system·(glibc) | 740 | ##·tzcode·source:·system·(glibc) |
| 741 | ##· | 741 | ##· |
| 742 | ##·attached·base·packages: | 742 | ##·attached·base·packages: |
| 743 | ##·[1]·stats·····graphics··grDevices·utils·····datasets··methods···base····· | 743 | ##·[1]·stats·····graphics··grDevices·utils·····datasets··methods···base····· |
| 744 | ##· | 744 | ##· |
| 745 | ##·other·attached·packages: | 745 | ##·other·attached·packages: |
| 746 | ##·[1]·markdown_1.13·knitr_1.50··· | 746 | ##·[1]·markdown_1.13·knitr_1.50··· |