library(TCGAbiolinks)
library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlibrary(DT)TCGA 数据获取
本笔记的目的为记录获取 TCGA 中乳腺癌的转录组测序数据，为后续的分析做准备。
载入所需包
使用getGDCprojects()$project_id得到各个癌种的项目id。
getGDCprojects()$project_id [1] "CGCI-HTMCP-CC" "TARGET-AML"
[3] "GENIE-JHU" "GENIE-MSK"
[5] "GENIE-VICC" "GENIE-MDA"
[7] "TCGA-MESO" "TARGET-ALL-P3"
[9] "TCGA-UVM" "TCGA-KICH"
[11] "TARGET-WT" "TARGET-OS"
[13] "TCGA-DLBC" "GENIE-UHN"
[15] "APOLLO-LUAD" "CDDP_EAGLE-1"
[17] "EXCEPTIONAL_RESPONDERS-ER" "MP2PRT-WT"
[19] "CGCI-HTMCP-DLBCL" "CMI-MPC"
[21] "WCDT-MCRPC" "TCGA-CHOL"
[23] "TCGA-UCS" "TCGA-PCPG"
[25] "CPTAC-2" "TCGA-CESC"
[27] "TCGA-LIHC" "TCGA-ACC"
[29] "CMI-MBC" "TCGA-BRCA"
[31] "CPTAC-3" "TCGA-COAD"
[33] "TCGA-GBM" "TCGA-TGCT"
[35] "NCICCR-DLBCL" "TCGA-LGG"
[37] "FM-AD" "GENIE-GRCC"
[39] "CTSP-DLBCL1" "TARGET-CCSK"
[41] "GENIE-NKI" "TARGET-ALL-P1"
[43] "MATCH-N" "TRIO-CRU"
[45] "CMI-ASC" "TARGET-RT"
[47] "ORGANOID-PANCREATIC" "MATCH-Z1D"
[49] "MATCH-B" "VAREPOP-APOLLO"
[51] "MATCH-Q" "BEATAML1.0-CRENOLANIB"
[53] "MATCH-Y" "OHSU-CNL"
[55] "CGCI-HTMCP-LC" "TARGET-NBL"
[57] "TCGA-SARC" "TCGA-PAAD"
[59] "TCGA-LUAD" "TCGA-PRAD"
[61] "MP2PRT-ALL" "TCGA-LUSC"
[63] "TCGA-LAML" "TCGA-SKCM"
[65] "HCMI-CMDC" "BEATAML1.0-COHORT"
[67] "TCGA-BLCA" "TCGA-READ"
[69] "TCGA-UCEC" "TCGA-THCA"
[71] "TCGA-OV" "TCGA-KIRC"
[73] "MMRF-COMMPASS" "GENIE-DFCI"
[75] "TCGA-HNSC" "TCGA-ESCA"
[77] "CGCI-BLGSP" "TARGET-ALL-P2"
[79] "TCGA-STAD" "REBC-THYR"
[81] "TCGA-KIRP" "TCGA-THYM" TCGA 的数据种类有以下几种：
Simple Nucleotide Variation
Transcriptome Profiling
Biospecimen
Sequencing Reads
Copy Number Variation
Clinical
DNA Methylation
Combined Nucleotide Variation
……
可以使用TCGAbiolinks:::getProjectSummary(project)查看project中有哪些数据类型，如查询 “TCGA-LIHC”，有7种数据类型，case_count为病人数，file_count为对应的文件数。要下载表达谱，可以设置data.category="Transcriptome Profiling"
TCGAbiolinks:::getProjectSummary("TCGA-BRCA")$file_count
[1] 58776
$data_categories
file_count case_count data_category
1 7562 1098 Sequencing Reads
2 5316 1098 Biospecimen
3 12066 1098 Copy Number Variation
4 17111 1098 Simple Nucleotide Variation
5 4876 1097 Transcriptome Profiling
6 3714 1097 DNA Methylation
7 2288 1098 Clinical
8 4924 1095 Structural Variation
9 919 881 Proteome Profiling
$case_count
[1] 1098
$file_size
[1] 1.813754e+14仅查看 TCGA 癌症的名称：
projects <- TCGAbiolinks::getGDCprojects()$project_id
projects <- projects[grepl('^TCGA', projects, perl=TRUE)]
projects [1] "TCGA-MESO" "TCGA-UVM" "TCGA-KICH" "TCGA-DLBC" "TCGA-CHOL" "TCGA-UCS"
[7] "TCGA-PCPG" "TCGA-CESC" "TCGA-LIHC" "TCGA-ACC" "TCGA-BRCA" "TCGA-COAD"
[13] "TCGA-GBM" "TCGA-TGCT" "TCGA-LGG" "TCGA-SARC" "TCGA-PAAD" "TCGA-LUAD"
[19] "TCGA-PRAD" "TCGA-LUSC" "TCGA-LAML" "TCGA-SKCM" "TCGA-BLCA" "TCGA-READ"
[25] "TCGA-UCEC" "TCGA-THCA" "TCGA-OV" "TCGA-KIRC" "TCGA-HNSC" "TCGA-ESCA"
[31] "TCGA-STAD" "TCGA-KIRP" "TCGA-THYM"数据下载
查询所需数据
GDCquery()筛选我们需要的数据，TCGAbiolinks包下载 TCGA 数据进行表达差异分析-乳腺癌案例
query <- GDCquery(project = "TCGA-BRCA",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts")--------------------------------------o GDCquery: Searching in GDC database--------------------------------------Genome of reference: hg38--------------------------------------------oo Accessing GDC. This might take a while...--------------------------------------------ooo Project: TCGA-BRCA--------------------oo Filtering results--------------------ooo By data.typeooo By workflow.type----------------oo Checking data----------------ooo Checking if there are duplicated casesooo Checking if there are results for the query-------------------o Preparing output-------------------# 获取样本的 barcode
samplesDown <- getResults(query,cols=c("cases"))根据组织类型筛选数据
# 从samplesDown中筛选出TP（实体肿瘤）样本的barcodes
# TCGAquery_SampleTypes(barcode, typesample)
# TP代表PRIMARY SOLID TUMOR；NT-代表Solid Tissue Normal
##此处共检索出371个TP样本barcodes
dataSmTP <- TCGAquery_SampleTypes(barcode = samplesDown,
typesample = "TP")
# 从samplesDown中筛选出NT(正常组织)样本的barcode
#此处共检索出50个NT样本barcodes
dataSmNT <- TCGAquery_SampleTypes(barcode = samplesDown,
typesample = "NT")TCGA 样本类型及其缩写：
| TP | PRIMARY SOLID TUMOR | TM | Metastatic |
|---|---|---|---|
| TR | RECURRENT SOLID TUMOR | TAM | Additional Metastatic |
| TB | Primary Blood Derived Cancer-Peripheral Blood | THOC | Human Tumor Original Cells |
| TRBM | Recurrent Blood Derived Cancer-Bone Marrow | TBM | Primary Blood Derived Cancer-Bone Marrow |
| TAP | Additional-New Primary | NB | Blood Derived Normal |
| NT | Solid Tissue Normal | NBC | Buccal Cell Normal |
| NEBV | EBV Immortalized Normal | NBM | Bone Marrow Normal |
设置barcodes参数，筛选符合要求的 371 个肿瘤样本数据和50正常组织数据：
queryDown <- GDCquery(project = "TCGA-BRCA",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts",
barcode = c(dataSmTP, dataSmNT))--------------------------------------o GDCquery: Searching in GDC database--------------------------------------Genome of reference: hg38--------------------------------------------oo Accessing GDC. This might take a while...--------------------------------------------ooo Project: TCGA-BRCA--------------------oo Filtering results--------------------ooo By data.typeooo By workflow.typeooo By barcode----------------oo Checking data----------------ooo Checking if there are duplicated casesooo Checking if there are results for the query-------------------o Preparing output-------------------下载数据
GDCdownload(queryDown,method = "api", directory = "GDCdata",
files.per.chunk = 100)Downloading data for project TCGA-BRCAOf the 1224 files for download 1224 already exist.All samples have been already downloaded数据准备与保存
GDCprepare()将前面GDCquery()的结果准备成R语言可处理的SE（SummarizedExperiment）文件：
dataPrep <- GDCprepare(
query = queryDown,
save = TRUE,
save.filename = "BRCA.rds"
)
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|====================================================|100% Completed after 1 m Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix 'paper_' brca subtype information from:doi.org/10.1016/j.ccell.2018.03.014Available assays in SummarizedExperiment :
=> unstranded
=> stranded_first
=> stranded_second
=> tpm_unstrand
=> fpkm_unstrand
=> fpkm_uq_unstrand=> Saving file: BRCA.rds=> File savedGDCprepare()中的参数：
| 参数 | 用法 |
|---|---|
| query | 来自GDCquery的结果 |
| save | 是否将结果保存为RData object，默认为TRUE |
| save.filename | 文件名，如果没有设置，系统将默认设置 |
| directory | 文件数据的文件夹，默认为"GDCdata" |
| summarizedExperiment | 是否生成summarizedExperiment对象，默认TRUE |
至此已经保存好了乳腺癌的转录组数据，以用于下游的处理与分析。