TCGA数据下载：R包RTCGAToolbox介绍

ypgao 2018-04-05

展开全文

前面介绍了3种获取TCGA数据的方法：使用TCGA2STAT、TCGAbiolinks、RTCGA。这里再介绍一个包：RTCGAToolbox包，这个包是我最为推荐的，原因是我使用时它下载数据最快、最为稳定可靠。

RTCGAToolbox下载方法

## try http:// if https:// URLs are not supported
source("https:///biocLite.R")
biocLite("RTCGAToolbox")1
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帮助文档：
http:///packages/release/bioc/manuals/RTCGAToolbox/man/RTCGAToolbox.pdf

可下载的数据请参考帮助文档或博客TCGA2STAT。

案例介绍

#包下载
source("https:///biocLite.R")
biocLite("RTCGAToolbox")
#加载包
library(RTCGAToolbox)

#哪些癌症数据可以下载
> getFirehoseDatasets()
 [1] "ACC"      "BLCA"     "BRCA"     "CESC"     "CHOL"     "COADREAD" "COAD"     "DLBC"     "ESCA"    
[10] "FPPP"     "GBMLGG"   "GBM"      "HNSC"     "KICH"     "KIPAN"    "KIRC"     "KIRP"     "LAML"    
[19] "LGG"      "LIHC"     "LUAD"     "LUSC"     "MESO"     "OV"       "PAAD"     "PCPG"     "PRAD"    
[28] "READ"     "SARC"     "SKCM"     "STAD"     "STES"     "TGCT"     "THCA"     "THYM"     "UCEC"    
[37] "UCS"      "UVM"     

#数据库中更新时间
> getFirehoseRunningDates()
 [1] "20151101" "20150821" "20150601" "20150402" "20150204" "20141206" "20141017" "20140902" "20140715" 
 [10] "20140614" "20140518" "20140416" "20140316" "20140215" "20140115" "20131210" "20131114" "20131010"
[19] "20130923" "20130809" "20130715" "20130623" "20130606" "20130523" "20130508" "20130421" "20130406"
[28] "20130326" "20130309" "20130222" "20130203" "20130116" "20121221" "20121206" "20121114" "20121102"
[37] "20121024" "20121020" "20121018" "20121004" "20120913" "20120825" "20120804" "20120725" "20120707"
[46] "20120623" "20120606" "20120525" "20120515" "20120425" "20120412" "20120321" "20120306" "20120217"
[55] "20120124" "20120110" "20111230" "20111206" "20111128" "20111115" "20111026"


#下载所需要的数据，这里以乳腺癌为例，数据下载完后会直接放在你的工作目录，不同地方下载的速度不一样，我这里等待了好久才下完。
brcaData = getFirehoseData (dataset="READ", runDate="20150402",forceDownload = TRUE,
                            Clinic=TRUE, Mutation=TRUE)

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