上一篇我们的基因体时代-AI, Data和生物资讯 Day24- 使用tidyverse观念来分析基因资料:plyranges分享加入了tidyverse观念的资料处理方法，算是这五年Ｒ里面主流的一个语法，而创建IRange/GRange架构的开发者Michael Lawrence也利用tidyverse的原则来建立plyranges包，我们持续整合前面方法搭配plyranges来进行基因注释资料的分享。

使用AnnotationHub:更多的基因注释和序列资料

之前有介绍过使用AnnotationDbi的介面来对资料封包做存取，分别可以使用columns, keytypes等函数来了解这个资料包有什麽内容，以及可以用什麽资讯来检索，这边介绍获取更大资料的方式，可以利用AnnotationHub，就其目前的资料，至少包含有57231笔资料集可以使用，里面有来自52个组织或是项目的资料包含如UCSC, Ensembl, NIH, EMBL-EBI, NCBI, ENCODE Project, Broad Institute, Stanford等等，来自2643种物种的资讯，里面有人类、细菌、霉菌、寄生虫等等，资料格式有28种，从单纯的列表(list)、资料格(data.frame)到我们前几天分享的GRanges, TxDb甚至序列资料(TwoBit)等，非常丰富。

## load library
library(AnnotationHub)
## construct annotationHub
ah <- AnnotationHub()
## see the elements and resources in the annotationHub
length(ah)
snapshotDate(ah)
mcols(ah)

我们可以使用mcols来看这些resource的一些细节，比如title, dataprovider, species, taxonomyi, genome, description, maintainer, rdatadateadded, preparerclass等等。

> ah %>% mcols() %>% colnames
 [1] "title"  "dataprovider"       "species"            "taxonomyid"         "genome" 
 [6] "description"  "coordinate_1_based" "maintainer" "rdatadateadded"  "preparerclass"  
[11] "tags" "rdataclass"   "rdatapath"  "sourceurl" "sourcetype" 

这边我们可以进一步利用query来搜寻资源里面包含有特定字串描述的资源，并且来阅览一下他们的内容

ahs.gtf.resources   <- query(ah, c("Homo sapiens", "GRCh38", "gtf"))

ahs.2bit.resources  <- query(ah, c("Homo sapiens", "GRCh38", "2bit"))

ahs.gtf.resources.df    <- data.frame(ah_id    = ahs.gtf.resources$ah_id,
                                      title    = ahs.gtf.resources$title,
                                      provider = ahs.gtf.resources$dataprovider,
                                      genome   = ahs.gtf.resources$genome,
                                      date     = ahs.gtf.resources$rdatadateadded,
                                      dataType = ahs.gtf.resources$rdataclass)

ahs.2bit.resources.df   <- data.frame(ah_id    = ahs.2bit.resources$ah_id,
                                      title    = ahs.2bit.resources$title,
                                      provider = ahs.2bit.resources$dataprovider,
                                      genome   = ahs.2bit.resources$genome,
                                      date     = ahs.2bit.resources$rdatadateadded,
                                      dataType = ahs.2bit.resources$rdataclass)

> ahs.2bit.resources.df %>% head
    ah_id                                            title provider genome       date   dataType
1 AH49722                Homo_sapiens.GRCh38.cdna.all.2bit  Ensembl GRCh38 2015-12-28 TwoBitFile
2 AH49723    Homo_sapiens.GRCh38.dna.primary_assembly.2bit  Ensembl GRCh38 2015-12-28 TwoBitFile
3 AH49724 Homo_sapiens.GRCh38.dna_rm.primary_assembly.2bit  Ensembl GRCh38 2015-12-28 TwoBitFile
4 AH49725 Homo_sapiens.GRCh38.dna_sm.primary_assembly.2bit  Ensembl GRCh38 2015-12-28 TwoBitFile
5 AH49726                   Homo_sapiens.GRCh38.ncrna.2bit  Ensembl GRCh38 2015-12-28 TwoBitFile
6 AH50067                Homo_sapiens.GRCh38.cdna.all.2bit  Ensembl GRCh38 2015-12-29 TwoBitFile

最後，我们可以利用他们的ah_id来进行下载，语法相当单纯，比如我们想要下载一笔名为Homo_sapiens.GRCh38.cdna.all.2bit的资料，我们直接用他的ah_id即为AH49722，用下面的语法即可

Homo.sapiens.GRCh38.cdna.2bit <- ahs.2bit.resources[["AH49722"]]

阅读参考:
Pagès H, Carlson M, Falcon S, Li N (2021). AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor. R package version 1.54.1, https://bioconductor.org/packages/AnnotationDbi.

Morgan M, Pagès H, Obenchain V, Hayden N (2021). Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. R package version 2.8.0, https://bioconductor.org/packages/Rsamtools.

Pagès H (2021). BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs. R package version 1.60.0, https://bioconductor.org/packages/BSgenome.

Morgan M (2019). AnnotationHub: Client to access AnnotationHub resources. R package version 2.18.0.

2017.[Adavanced GenomicRanges, RtrackLayer and Rsamtools]
(https://combine-australia.github.io/2017-05-19-bioconductor-melbourne/AdvGRanges_Rtracklayer_Rsamtools.html)

这个月的规划贴在这篇文章中我们的基因体时代-AI, Data和生物资讯 Overview，也会持续调整！我们的基因体时代是我经营的部落格，如有对於生物资讯、检验医学、资料视觉化、R语言有兴趣的话，可以来交流交流！