需要用到DNA甲基化芯片的注释包IlluminaHumanMethylation450k.db，但是用BiocManager安装会报错“is not available”.
搜到了生信技能树的文章《如果这个R包真的不存在了肿么办》，但只谈到包被删除了之前是存在的...
https://cloud.tencent.com/developer/article/1508953
也就是说，这个包是被删除了，在 https://bioconductor.org/about/removed-packages/
可以看到是很早之前，就被删除了。
如何安装被移除的R包呢
这个其实跟我之前讲解的如何安装旧版R包有异曲同工之妙。
留给读者解决吧，相信你粉了我们生信技能树这么久，这一点实力，还是可以有的！
下载IlluminaHumanMethylation450k.db包的源码压缩包并安装。
https://www.bioconductor.org/packages//2.12/data/annotation/html/IlluminaHumanMethylation450k.db.html
# 解压
tar -xf IlluminaHumanMethylation450k.db_2.0.7.tar.gz
提前安装依赖包
# 'BiocGenerics','S4Vectors','IRanges', 'Biobase', 'BiocGenerics', 'AnnotationDbi', 'org.Hs.eg.db', 'AnnotationForge'
# "bit", "plogr", "blob", "bit64", 'S4Vectors', 'RSQLite', 'DBI','RSQLite','remotes'
修改源代码
修改IlluminaHumanMethylation450k.db/R/zzz.R中的源码
AnnotationForge:::createSimpleBimap
替换为下边的代码，因为报错找不到 createSimpleBimap；发现包换了
AnnotationDbi::createSimpleBimap
正式安装
library(remotes)
remotes::install_local("IlluminaHumanMethylation450k.db")
安装完才发现有替代的包 "FDb.InfiniumMethylation.hg19"...
Warning message:
'IlluminaHumanMethylation450k.db' is deprecated.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Deprecated")
查看有哪些注释信息
# could not find function "dbGetQuery"
library(DBI)
library(IlluminaHumanMethylation450k.db)
IlluminaHumanMethylation450k.db::IlluminaHumanMethylation450k()
# IlluminaHumanMethylation450kACCNUM has 365088 mapped keys (of 365088 keys)
# IlluminaHumanMethylation450kALIAS2PROBE has 74043 mapped keys (of 143558 keys)
# IlluminaHumanMethylation450kCHR has 331568 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kCHRLENGTHS has 93 mapped keys (of 640 keys)
# IlluminaHumanMethylation450kCHRLOC has 331443 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kCHRLOCEND has 331443 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kENSEMBL has 319028 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kENSEMBL2PROBE has 18604 mapped keys (of 39708 keys)
# IlluminaHumanMethylation450kENTREZID has 331594 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kENZYME has 38658 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kENZYME2PROBE has 925 mapped keys (of 975 keys)
# IlluminaHumanMethylation450kGENENAME has 331594 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kGO has 302014 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kGO2ALLPROBES has 13290 mapped keys (of 22963 keys)
# IlluminaHumanMethylation450kGO2PROBE has 10083 mapped keys (of 18933 keys)
# IlluminaHumanMethylation450kMAP has 330724 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kOMIM has 240300 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kPATH has 97051 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kPATH2PROBE has 214 mapped keys (of 229 keys)
# IlluminaHumanMethylation450kPMID has 330468 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kPMID2PROBE has 275464 mapped keys (of 754859 keys)
# IlluminaHumanMethylation450kREFSEQ has 331594 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kSYMBOL has 331594 mapped keys (of 482931 keys)
# IlluminaHumanMethylation450kUNIPROT has 316916 mapped keys (of 482931 keys)
# 探针与基因名的对应关系
IlluminaHumanMethylation450kSYMBOL
# 染色体信息
IlluminaHumanMethylation450kMAP
IlluminaHumanMethylation450kCHRLOC
IlluminaHumanMethylation450kCHRLOCEND
IlluminaHumanMethylation450kCHRLENGTHS
提取探针与基因名的对应关系
a=IlluminaHumanMethylation450k.db::IlluminaHumanMethylation450kSYMBOL
b=as.data.frame(a)
head(b)
# probe_id symbol
# 1 cg03123289 A1BG
# 2 cg03630821 A1BG
# 3 cg10734734 A1BG
# 4 cg11001216 A1BG
# 5 cg14222245 A1BG
# 6 cg22286978 A1BG
FDb.InfiniumMethylation.hg19的注释信息
FDb.InfiniumMethylation.hg19是替代包，所以也安装比较下区别
BiocManager::install("FDb.InfiniumMethylation.hg19")
library(FDb.InfiniumMethylation.hg19)
FDb.InfiniumMethylation.hg19::FDb.InfiniumMethylation.hg19
# FeatureDb object:
# | Db type: FeatureDb
# | Supporting package: GenomicFeatures
# | data_nrow: 487173
# | Db created by: GenomicFeatures package from Bioconductor
# | Creation time: 2013-05-07 17:02:12 -0700 (Tue, 07 May 2013)
# | GenomicFeatures version at creation time: 1.13.2
# | RSQLite version at creation time: 0.11.3
# | DBSCHEMAVERSION: 1.0
# | Data source: NCBI/GEO and dbSNP
# | Genome: hg19
# | Resource: Illumina Infinium DNA methylation probes, mapped to hg19
# | Genus and Species: Homo sapiens
# | URL: ftp://ftp.illumina.com
探针信息
hm450 <- FDb.InfiniumMethylation.hg19::get450k()
as.data.frame(hm450) %>% head()
seqnames start end width strand addressA addressB channel platform percentGC sourceSeq probeType probeStart probeEnd probeTarget
cg04913815 chr16 60438 60439 2 * 24771476 "" Both HM450 0.58 TTTCGGTGGTACTGCGAAGGCAGAGCAGAGTTCTGCTCAGGTCAGACCCG cg 60438 60487 60438
cg01686861 chr16 60748 60749 2 * 36644319 45624454 Red HM450 0.76 CGCCCCCAGGCCGGCGCCGTGCGACTTTGCTCCTGCAACACACGCCCCCC cg 60700 60749 60748
cg05558259 chr16 61085 61086 2 * 65765435 "" Both HM450 0.56 CAGCTAGGGACATTGCAGGCTCCTCTTGCTCAAAGTGTAGTGGCAGCACG cg 61037 61086 61085
cg26978960 chr16 62460 62461 2 * 28717484 "" Both HM450 0.66 CGGCCCAGTAGAGCCCTAGGGGTGACGCCACTCCCACTCACTGTCGACTC cg 62412 62461 62460
cg03792876 chr16 73243 73244 2 * 42725455 "" Both HM450 0.64 ATGGAGGCTTGGGCGGGTCACCCCCAGTGCAGGCCAAGATGCAGGTTACG cg 73195 73244 73243
cg09699726 chr16 91602 91603 2 * 34629364 "" Both HM450 0.68 GCACTAGAGCCCCAGGGCCAGGGGAGACCCAGCATCCAAGGTGCACCACG cg 91554 91603 91602
探针最近的基因、转录本、TSS
gene <- FDb.InfiniumMethylation.hg19::getNearestGene(hm450)
head(gene)
# queryHits subjectHits distance nearestGeneSymbol
# cg04913815 1 666 1115 DDX11L10
# cg01686861 2 666 805 DDX11L10
# cg05558259 3 666 468 DDX11L10
# cg26978960 4 666 0 DDX11L10
# cg03792876 5 666 9152 DDX11L10
# cg09699726 6 14930 5375 POLR3K
transcript <- FDb.InfiniumMethylation.hg19::getNearestTranscript(hm450)
head(transcript)
# queryHits subjectHits distance nearestGeneSymbol nearestTranscript
# cg04913815 1 1033 1115 DDX11L10 uc010bqm.2
# cg01686861 2 1033 805 DDX11L10 uc010bqm.2
# cg05558259 3 1033 468 DDX11L10 uc010bqm.2
# cg26978960 4 1033 0 DDX11L10 uc010bqm.2
# cg03792876 5 1033 9152 DDX11L10 uc010bqm.2
# cg09699726 6 40773 5375 POLR3K uc002cfi.2
tss <- FDb.InfiniumMethylation.hg19::getNearestTSS(hm450)
head(tss)
# queryHits subjectHits distance nearestGeneSymbol nearestTranscript
# cg04913815 1 799 1115 DDX11L10 uc010bqm.2
# cg01686861 2 799 805 DDX11L10 uc010bqm.2
# cg05558259 3 799 468 DDX11L10 uc010bqm.2
# cg26978960 4 799 904 DDX11L10 uc010bqm.2
# cg03792876 5 799 11687 DDX11L10 uc010bqm.2
# cg09699726 6 24097 12028 POLR3K uc002cfi.2
网友评论