本课程的材料要求R版本3.2和Bioconductor版本3.2
stopifnot(getRversion() >= '3.2' && getRversion() < '3.3'， BiocInstaller::biocVersion() == "3.2")TxDb包例如,“{r Biocpkg (TxDb.Hsapiens.UCSC.hg19.knownGene)}
txdb <- txdb . hapiens . ucsc .hg19. knowngeneknownGene txdb# # TxDb对象:# # # Db型:TxDb支持包:# # # # # # GenomicFeatures数据来源:UCSC基因组:# # # # # # hg19生物:智人# # #分类ID: 9606 # # # UCSC的表:knownGene # # #资源URL: http://genome.ucsc.edu/ # # #的基因类型ID: Entrez基因ID # # #完整数据集:是的# # # miRBase构建ID: GRCh37 # # # transcript_nrow:82960 # # # exon_nrow: 289969 # # # cds_nrow: 237533 # # # Db由:GenomicFeatures包从Bioconductor # # #创建时间:2015-10-07 18:11:28 + 0000(2015年10月结婚,07年)# # # GenomicFeatures版本在创建的时候:1.21.30创建时间:# # # RSQLite版本1.0.0 # # # DBSCHEMAVERSION: 1.1方法(类=类(txdb))## [1] annotatedDataFrameFrom asBED asGFF as。表# # [5]assayData assayData < - cdsByOverlaps cdsBy # # [9] cd胁迫列结合# #[13]内容dbconn dbfile dbInfo # #[17]该dbschema disjointExons距离# # [21]$ < - $ exonsByOverlaps exonsBy # #[25]外显子ExpressionSet extractUpstreamSeqs featureNames < - # # [29] featureNames fiveUTRsByTranscript基因初始化# # [33]## [49] revmap sample sampleNames<- sampleNames ## [53] saveDb select seqinfo seqlevels0 ## [57] seqlevels<- show species storageMode<- ## [61]storageMode summarizeVariants taxonomyId threeUTRsByTranscript ## [65] transcriptsByOverlaps transcriptsBy transcripts tRNAs ## [69] updateObject ## see '?方法，用于访问帮助和源代码TxDb对象
dbfile (txdb)GenomicFeatures:: makeTxDbFrom * ()访问基因模型
外显子(),成绩单(),基因(),cd ()(编码序列)发起人()和朋友exonsBy ()&朋友-外显子由基因，转录，…keytypes (),列(),键(),select (),mapIds ()外显子(txdb)与289969年# #农庄对象范围和1元数据列:# # seqnames范围链| exon_id # # < Rle > < IRanges > < Rle > | <整数> # # [1]chr1(11874、12227)+ | 1 # # [2]chr1(12595、12721)+ | 2 # # [3]chr1(12613、12721)+ | 3 # # [4]chr1(12646、12697)+ | 4 # # [5]chr1(13221、14409)+ | 5 ## ... ... ... ... ... ...# # [289965] chrUn_gl000241(35706、35859)- | 289965 # # [289966]chrUn_gl000241(36711、36875)- | 289966 # # [289967]chrUn_gl000243(11501、11530)+ | 289967 # # [289968]chrUn_gl000243(13608、13637)+ | 289968 # # [289969]chrUn_gl000247(5787、5816)- | 289969 ## ------- ## seqinfo: 93从hg19基因组序列(1循环)exonsBy (txdb tx)## $1 GRanges object of length 82960: ## $1 GRanges object with 3 range and 3 metadata column# # seqnames范围链| exon_id exon_name exon_rank # # < Rle > < IRanges > < Rle > | <整数> <人物> <整数> # # [1]chr1(11874、12227)+ | 1 < NA > 1 # # [2] chr1(12613、12721)+ | 3 < NA > 2 # # [3] chr1(13221、14409)+ | 5 < NA > 3 # # # # # # 2美元农庄对象与范围和3元数据列:# # seqnames范围链| exon_id exon_name exon_rank # # [1] chr1(11874、12227)+ | 1 < NA > 1 # # [2] chr1(12595、12721)+ | 2 < NA > 2 # # [3] chr1(13403、14409)+ | 6 < NA > 3 # # # # # # 3美元农庄对象与范围和3元数据列:## seqnames ranges strand | exon_id exon_name exon_rank ## [1] chr1 [11874, 12227] + | 1 1 ## [2] chr1 [12646, 12697] + | 4 2 ## [3] chr1 [13221, 14409] + | 5 3 ## ##…## <82957 more elements> ## ------- ## seqinfo:来自hg19基因组的93个序列(1个循环) BSgenome包例如,“{r Biocpkg (BSgenome.Hsapiens.UCSC.hg19)}
BSgenome.Hsapiens.UCSC.hg19 (BSgenome.Hsapiens.UCSC.hg19)hg19 getSeq(基因外显子(txdb) [1:10])## DNAStringSet实例的长度100 ##宽度seq ## [1] 354 cttgccgtcagccttttctttttgacctcttctttttctgttcatgt…##[2] 127…GACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAG # # [3] 109 GTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCT…GACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAG # # [4] 52 CATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTT # # [5] 1189 GCAGGGCCATCAGGCACCAAAGGGATTCTGCCAGCATAGTGCT…Acagctagagatcctttattaaaagcacactgttggtttctg ## ... ... ...## [96] 251 cccgtccccggcgcgcgcgcccccccccccccccccccccccccccccctcgc…## [97] 262 gttcgggtctggcttgtacttgaagggcaaagacctggccc…TCACCCTGCGGAACCTGGAGGAGGTGGAGTTCTGTGTGGAAG 48 ATAAACCCGGGACCCACTTCACTCCAGTGCCTCCGACGCCTCCTGATG # # # # [98] [99] 216 CGTGCCGGGGAATGCTGTGCGGCTTCGGCGCCGTGTGCGAGCC…GCCAGCAGCGCCGCATCCGCCTGCTCAGCCGCGGGCCGTGCG # # 225 GCTCGCGGGACCCCTGCTCCAACGTGACCTGCAGCTTCGGCAG…CCCGCCAGGAGAATGTCTTCAAGAAGTTCGACGGCCCTTGTG [100]OrgDb图书馆(org.Hs.eg.db) org.Hs.eg.db# # OrgDb对象:# # | DBSCHEMAVERSION: 2.1 # # | Db型:OrgDb # # |支持包:AnnotationDbi # # | DBSCHEMA: HUMAN_DB # # |生物:智人# # |物种:人类# # | EGSOURCEDATE: 2015 - sep27 # # | EGSOURCENAME: Entrez基因# # | EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA # # | CENTRALID:如# # | TAXID: 9606 # # | GOSOURCENAME:基因本体论# # | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ # # | GOSOURCEDATE: 20150919 # # | GOEGSOURCEDATE: 2015 - sep27 # # | GOEGSOURCENAME: Entrez基因# # | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA # # | KEGGSOURCENAME: KEGG基因组# # | KEGGSOURCEURL:## | KEGGSOURCEDATE: 2011-Mar15 ## | GPSOURCENAME: UCSC基因组生物信息学(智人)## | GPSOURCEURL: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19 ## | GPSOURCEDATE: 2010-Mar22 ## | ENSOURCEDATE: 2015-Jul16 ## | ENSOURCENAME: Ensembl ## | ENSOURCEURL:ftp://ftp.ensembl.org/pub/current_fasta ## | UPSOURCENAME: Uniprot ## | UPSOURCEURL: http://www.UniProt.org/ ## | UPSOURCEDATE: 2015年10月9日星期五19:54:03## ##请参阅:help('select')查看使用信息OrgDb对象
TxDbkeytypes (),列(),键(),select (),mapIds ()select ()
按键类型规格
选择(org.Hs.eg.db, c(“BRCA1”、“PTEN”),c(“ENTREZID”、“GENENAME”),“象征”)## 'select()'返回键和列之间的1:1映射## # ENTREZID基因## # 1 BRCA1 672乳腺癌1，早发## # 2 PTEN 5728磷酸酶和紧张素同源物keytypes (org.Hs.eg.db)## [1] " accnum " " alias " " ensembl " " ensemblprot " " ensembltrans " " entrezid " ## [7] " enzyme " " evidence " " evidence all " " genename " " go " " goall " ## [13] " ipi " " map " " omim " " ontology " " ontology " " path " ## [19] " pfam " " mid " " prosite " " refseq " " symbol " " ucsckg " ## [25] " unigene " " uniprot "列(org.Hs.eg.db)## [1] " accnum " " alias " " ensembl " " ensemblprot " " ensembltrans " " entrezid " ## [7] " enzyme " " evidence " " evidence all " " genename " " go " " goall " ## [13] " ipi " " map " " omim " " ontology " " ontology " " path " ## [19] " pfam " " mid " " prosite " " refseq " " symbol " " ucsckg " ## [25] " unigene " " uniprot "相关功能
mapIds ()-从一个标识符映射到另一个标识符的特殊情况OrganismDb对象:结合org . *,TxDb。*，以及其他易于访问的注释资源
库(Homo.sapiens)##现在直接获得GODb对象##现在直接获得OrgDb对象##现在直接获得TxDb对象选择(Homo。智人,c(“BRCA1”、“PTEN”),c(“TXNAME”、“TXCHROM”,“TXSTART”、“TXEND”),“象征”)## select()返回1:很多键和列之间的映射##符号TXNAME TXCHROM TXSTART TXEND ## 1 BRCA1 uc010whl。2 ch17 41196312 41276132 ## 2 BRCA1 uc002icp。4 chr17 41196312 41277340 ## 3 BRCA1 uc010whm。2 ch17 41196312 41277340 ## 4 BRCA1 uc002icu3 chr17 41196312 41277468 ## 5 BRCA1 uc010cyx3 chr17 41196312 41277468 ## 6 BRCA1 uc002icq。3 chr17 41196312 41277500 ## 7 BRCA1 uc002ict。3 chr17 41196312 41277500 ## 8 BRCA1 uc010whn。2 chr17 41196312 41277500 ## 9 BRCA1 uc010who。3.chr17 41196312 41277500 ## 10 BRCA1 uc010whp.2 chr17 41196312 41322420 ## 11 BRCA1 uc010whq.1 chr17 41215350 41256973 ## 12 BRCA1 uc002idc.1 chr17 41215350 41277468 ## 13 BRCA1 uc010whr.1 chr17 41215350 41277468 ## 14 BRCA1 uc002idd.3 chr17 41243117 41276132 ## 15 BRCA1 uc002ide.1 chr17 41243452 41256973 ## 16 BRCA1 uc010cyy.1 chr17 41243452 41277340 ## 17 BRCA1 uc010whs.1 chr17 41243452 41277468 ## 18 BRCA1 uc010cyz.2 chr17 41243452 41277500 ## 19 BRCA1 uc010cza.2 chr17 41243452 41277500 ## 20 BRCA1 uc010wht.1 chr17 41243452 41277500 ## 21 PTEN uc001kfb.3 chr10 89623195 89728532 ## 22 PTEN uc021pvw.1 chr10 89623195 89728532biomaRt,AnnotationHubhttp://biomart.org;Bioconductor包biomaRt
##需要上网!!库(biomaRt)头(listMarts(), 3) # #集市列表头(listDatasets (useMart(“运用”)),3)运用< - # # # #集市数据集完全指定的集市useMart(“运用”,数据集=“hsapiens_gene_ensembl”)负责人(listFilters(运用),3)# #过滤器myFilter < -“chromosome_name substr (filterOptions (myFilter运用),1,##集合和查询mart res <- getBM(attributes = myAttributes, filters = myFilter, values = myValues, mart = ensembl)其他网络资源
示例:集成“GTF”文件R/Bioconductor农庄和TxDb
library(AnnotationHub) hub <- AnnotationHub() hub query(hub, c(" ensemble bl"， "80"， "gtf")) ## ensgtf = display(hub) # visual choice hub["AH47107"] gtf <- hub[["AH47107"]] gtf txdb <- GenomicFeatures::makeTxDbFromGRanges(gtf)例如:non-model生物OrgDb包
library(AnnotationHub) hub <- AnnotationHub() query(hub， "OrgDb")示例:将路线图表基因组标记映射到hg38
路线图床文件如下农庄
查询(hub, c("EpigenomeRoadMap"， "E126"， "H3K4ME2")) E126 <- hub[["AH29817"]]UCSC ' liftOver '文件映射坐标
查询(中心,c(“hg19”、“hg38”,“chainfile”))链< -中心[[“AH14150”]]提升可能的一对多映射，所以农庄来GRangesList
library(rtracklayer) E126hg38 <- liftOver(E126, chain) E126hg38示例:从VCF文件中读取变体，并对已知的基因模型进行注解
##输入变量库(VariantAnnotation) fl <- system. php)##已知的基因模型库(txdb . haspises . ucsc .hg19. knowngene)编码<- locateVariants(rowRanges(vcf)， txdb . haspises . ucsc .hg19. knowngene)编码<- locateVariants(rowRanges(vcf)， txdb . haspises . ucsc .hg19. knowngene)。knownGene CodingVariants())头(编码)## GRanges对象有6个范围和9个元数据列:# # seqnames范围链|位置LOCSTART LOCEND QUERYID TXID # # < Rle > < IRanges > < Rle > | <因素> <整数> <整数> <整数> <人物> # # 1 chr22(50301422、50301422)- |编码939 939 24 75253 # # 2 chr22(50301476、50301476)25 - |编码885 885 75253 # # 3 chr22(50301488、50301488)26 - |编码873 873 75253 # # 4 chr22 (50301494,50301494] - |编码867 867 27 75253 ## 5 chr22[50301584, 50301584] - |编码777 777 28 75253 ## 6 chr22 [50302962，50302962] 57 - |编码698 698 75253 # # CDSID GENEID PRECEDEID FOLLOWID # # < IntegerList > <人物> < CharacterList > < CharacterList > # # 1 218562 79087 # 218562 # 79087 # 218562 # 79087 # 218562 # 79087 # 218562 # 79087 # # 6 218563 79087 ## ------- ## seqinfo: 1从一个未指明的基因组序列;没有seqlengths确认
核心(西雅图):Sonali Arora, Marc Carlson, Nate Hayden, Jim Hester, Valerie Obenchain, Hervé Pagès, Paul Shannon, Dan Tenenbaum。
本次报告中的研究由美国国家癌症研究所和美国国立卫生研究院的国家人类基因组研究所(奖励号为U24CA180996和U41HG004059)以及美国国家科学基金会(奖励号为1247813)资助。内容仅由作者负责，不一定代表国家卫生研究院或国家科学基金会的官方观点。
sessionInfo ()sessionInfo ()## R version 3.2.2 (2015-08-14) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux stretch/sid ## ## locale: ## [1] LC_CTYPE=en_US。utf - 8 LC_NUMERIC = C而= en_US。UTF-8 ## [4] LC_COLLATE=en_US。utf - 8 LC_MONETARY = en_US。utf - 8 LC_MESSAGES = en_US。UTF-8 ## [7] LC_PAPER=en_US。UTF-8 LC_NAME=C LC_ADDRESS= c# ## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US。## [1] stats4 parallel stats graphics grDevices utils datasets methods base ## ##其他附加包:# # # # [1] Homo.sapiens_1.3.1 GO.db_3.2.2 [3] OrganismDbi_1.11.43 biomaRt_2.25.3 # # [5] AnnotationHub_2.1.45 VariantAnnotation_1.15.34 # # [7] RNAseqData.HNRNPC.bam.chr14_0.7.0 GenomicAlignments_1.5.18 # # [9] Rsamtools_1.21.21 ALL_1.11.0 # # [11] org.Hs.eg.db_3.2.3 RSQLite_1.0.0 # # [13] DBI_0.3.1 ggplot2_1.0.1 # # [15] airway_0.103.1 limma_3.25.18 # #[17] DESeq2_1.9.51 RcppArmadillo_0.6.100.0.0 # # [19] Rcpp_0.12.1 BSgenome.Hsapiens.UCSC.hg19_1.4.0 # # [21] BSgenome_1.37.6 rtracklayer_1.29.28 # # [23] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.21.33 # # [25] AnnotationDbi_1.31.19 SummarizedExperiment_0.3.11 # # [27] Biobase_2.29.1 GenomicRanges_1.21.32 # # [29] GenomeInfoDb_1.5.16microbenchmark_1.4-2 ## [31] Biostrings_2.37.8 XVector_0.9.4 ## [33] IRanges_2.3.26 S4Vectors_0.7.23 ## [35] BiocGenerics_0.15.11 BiocStyle_1.7.9 ## ##通过命名空间加载(和没有附加):## [1] bitops_1.0-6 RColorBrewer_1.1-2 httr_1.0.0 ## [7] Hmisc_3.17-0 colorspace_1.2-6 nnet_7.3-11 ## [10] gridExtra_2.0.0 graph_1.47.2 formatR_1.2.1 ## [13] sandwich_2.3-4 labeling_0.3 scales_0.3.0 ## [16] mvtnorm_1.0-3 genefilter_1. 1.51.1 RBGL_1.45.1 ## [19] stringr_1.0.0 digest_0.6.8 foreign_0.8-66 ## [22]rmarkdown_0.8.1 htmltools_0.2.6 BiocInstaller_1.19.14 # # [25] shiny_0.12.2 zoo_1.7-12 BiocParallel_1.3.54 # # [28] acepack_1.3 4.7 - 3.3 rcurl_1.95 magrittr_1.5 # # [31] Formula_1.2-1 futile.logger_1.4.1 munsell_0.4.2 # # [34] proto_0.3-10 stringi_0.5-5 multcomp_1.4-1 # # [37] yaml_2.1.13 MASS_7.3-44 zlibbioc_1.15.0 # # [40] plyr_1.8.3 grid_3.2.2lattice_0.20-33 # # [43] splines_3.2.2 annotate_1.47.4 locfit_1.5 - 9.1 # # [46] knitr_1.11 geneplotter_1.47.0 reshape2_1.4.1 # # [49] codetools_0.2-14 futile.options_1.0.0 xml_3.98 - 1.3 # # [52] evaluate_0.8 latticeExtra_0.6-26 lambda.r_1.1.7 # # [55] httpuv_1.3.3 gtable_0.1.2 mime_0.4 # # [58] xtable_1.7-4 survival_2.38-3 cluster_2.0.3 # # [61] TH.data_1.0-6 interactiveDisplayBase_1.7.3