easyTCGA: 一行代码得到处理好的 TCGA 数据集

本笔记目的在于介绍如何使用easyTCGA

getmrnaexpr()获取数据集

getmrnaexpr(project)
  • project可以是任何 TCGA 项目

  • 自动下载并整理mRNAlncRNAcounts,tpm,fpkm共6种表达矩阵(直接从官网的原始数据提取,未进行任何修改,所以是没有经过log转换的),以及对应的临床信息,临床信息样本顺序和表达矩阵样本顺序完全一致,无需再次整理

  • 自动保存以上6种表达矩阵和临床信息到当前工作目录下的output_mRNA_lncRNA_expr文件夹下,并且同时保存rdatacsv两种文件格式

library(easyTCGA)

getmrnaexpr('TCGA-BRCA')
=> Querying begins. Make sure your network has access to GDC TCGA! 
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-BRCA
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oo Filtering results
--------------------
ooo By data.type
ooo By workflow.type
----------------
oo Checking data
----------------
ooo Checking if there are duplicated cases
ooo Checking if there are results for the query
-------------------
o Preparing output
-------------------
=> Downloading begins. Make sure your network has access to GDC TCGA! 
Downloading data for project TCGA-BRCA
Of the 1231 files for download 1231 already exist.
All samples have been already downloaded
=> Downloading ends. Preparing begins.

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|====================================================|100%                      Completed after 40 s 
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.2018.03.014
Available assays in SummarizedExperiment : 
  => unstranded
  => stranded_first
  => stranded_second
  => tpm_unstrand
  => fpkm_unstrand
  => fpkm_uq_unstrand
=> Saving file: output_mRNA_lncRNA_expr/TCGA-BRCA_expr.rdata
=> File saved
=> Preparing mRNA and lncRNA.
=> Successful.

其他函数使用方式一致:

  • getmrnaexpr_xena

    • 用于XENA网站下载的TCGA基因表达数据和临床信息的整理(仅限gdchub

    • 直接提供文件名即可,比如:TCGA-ACC.htseq_counts.tsv.gz, TCGA-ACC.htseq_fpkm.tsv.gzTCGA-ACC.GDC_phenotype.tsv.gz, TCGA-ACC.survival.tsv

    • 自动保存mRNAlncRNA表达矩阵和临床信息到当前工作目录下的output_mRNA_expr_xena文件夹下

    • id转换使用gtf 22,和XENA保持一致

    • (单独使用XENA的表达谱数据和直接用GDC官网数据相比没有任何优势)

  • getmirnaexpr

    • 只需要提供正确的TCGA project名字即可

    • 自动下载并整理miRNAcounts,rpm2种表达矩阵

    • 自动保存以上2种表达矩阵和对应的临床信息到当前工作目录下的output_miRNA_expr文件夹下,并且同时保存rdatacsv两种文件格式

    • 下载的数据为最新数据,和GDC TCGA官网保持一致

  • getsnvmaf

    • 只需要提供正确的TCGA project名字即可

    • 自动下载并整理TCGA MAF文件(masked somatic mutation)以及对应的临床信息,并自动保存到当前工作目录下的output_snv文件夹下

    • 输出结果可以直接通过maftools::read_maf()函数读取,无需再次整理

  • getcnv

    • 只需要提供正确的TCGA project名字即可

    • 自动下载并整理copy number variation数据;数据保存到当前工作目录下的output_cnv文件夹下

    • 下载的数据为最新数据,和GDC TCGA官网保持一致

  • getmethybeta

    • 只需要提供正确的TCGA project名字即可

    • 自动下载并整理450KDNA methylationbeta值矩阵,以及对应的临床信息,数量和顺序完全一致,无需再次整理

    • 自动整理探针信息,比如探针对应的gene symbol等,基于GRCh 38

    • 数据保存在当前工作目录下的output_methy文件夹下

    • 下载的数据为最新数据,和GDC TCGA官网保持一致

  • getpancancer_xena

    • 实现对泛癌数据的整理,支持TCGAGTEx,以及整合TCGA+GTEx

    • 只需提供相应的表达矩阵文件和样本信息文件即可

diff_analysis()差异分析

  • getmrnaexprgetmirnaexprgetmrnaexpr_xena函数无缝对接,直接使用其输出结果即可,无需任何整理(默认对tumor和normal组进行差异分析)

  • 支持count, tpm, fpkmGEO数据,如果是count则自动通过3个R包进行差异分析:DESeq2,edgeR,limma;如果是其他类型(tpm, fpkm基因表达芯片数据)会自动判断是否需要log2(x + 0.1)转换,然后使用limmawilcoxon test做差异分析

load("D://Rlearn/TCGA/output_mRNA_lncRNA_expr/TCGA-BRCA_expr.rdata")

data
class: RangedSummarizedExperiment 
dim: 60660 1231 
metadata(1): data_release
assays(6): unstranded stranded_first ... fpkm_unstrand fpkm_uq_unstrand
rownames(60660): ENSG00000000003.15 ENSG00000000005.6 ...
  ENSG00000288674.1 ENSG00000288675.1
rowData names(10): source type ... hgnc_id havana_gene
colnames(1231): TCGA-A7-A26E-01B-06R-A277-07
  TCGA-A2-A0CU-01A-12R-A034-07 ... TCGA-BH-A204-01A-11R-A157-07
  TCGA-A2-A0T1-01A-21R-A084-07
colData names(87): barcode patient ... paper_PARADIGM Clusters
  paper_Pan-Gyn Clusters
load("D://Rlearn/TCGA/output_mRNA_lncRNA_expr/TCGA-BRCA_mrna_expr_counts.rdata")

diff <- diff_analysis(
  mrna_expr_counts,
  project = "TCGA-BRCA",
  save = F
)
=> Running DESeq2
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 2832 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
=> Running limma voom
=> Running edgeR
=> Analysis done.

查看其中一个结果:

# deg_limma, deg_deseq2, deg_edger
head(diff[["deg_limma"]])
            logFC     AveExpr         t       P.Value     adj.P.Val        B
VEGFD   -5.916531 -0.54965746 -59.02417  0.000000e+00  0.000000e+00 818.4105
CA4     -6.798634 -2.44840657 -49.63097 2.696866e-296 2.303258e-292 668.1375
CD300LG -6.486092  0.07079663 -48.60172 7.288653e-289 4.149916e-285 651.3416
PAMR1   -3.947614  2.51132211 -48.28787 1.376454e-286 5.877802e-283 646.1626
LYVE1   -4.736294  1.50268285 -47.36443 7.280409e-280 2.487133e-276 630.6820
SCARA5  -6.386457  0.44002261 -45.87139 6.502987e-269 1.851292e-265 605.4932
        genesymbol
VEGFD        VEGFD
CA4            CA4
CD300LG    CD300LG
PAMR1        PAMR1
LYVE1        LYVE1
SCARA5      SCARA5

batch_survival() 生存分析

  • batch_survival

    • 自动进行logrank检验和单因素cox分析,默认基于最佳截点(P值最小)

    • getmrnaexprgetmirnaexpr函数无缝对接,直接使用其输出结果即可,无需任何整理

    • 支持count,tpm,fpkm3种格式的数据,如果是counts,则通过DESeq2::vst()进行转换,如果是tpm/fpkm,则进行log2(x + 0.1)转换

1surv <- batch_survival(
  mrna_expr_counts,
  clin = clin_info
)

2head(surv$res.logrank)
3head(surv$res.cox)
1
计算生存相关基因
2
查看结果(logrank)
3
查看结果(cox检验)

工作环境

devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.1 (2023-06-16 ucrt)
 os       Windows 11 x64 (build 22621)
 system   x86_64, mingw32
 ui       RTerm
 language (EN)
 collate  Chinese (Simplified)_China.utf8
 ctype    Chinese (Simplified)_China.utf8
 tz       Asia/Hong_Kong
 date     2023-11-06
 pandoc   3.1.9 @ C:/Users/HANWAN~1/AppData/Local/Pandoc/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package              * version    date (UTC) lib source
 abind                  1.4-5      2016-07-21 [1] CRAN (R 4.3.0)
 AnnotationDbi          1.62.2     2023-07-02 [1] Bioconductor
 Biobase                2.60.0     2023-04-25 [1] Bioconductor
 BiocFileCache          2.8.0      2023-04-25 [1] Bioconductor
 BiocGenerics           0.46.0     2023-04-25 [1] Bioconductor
 BiocParallel           1.34.2     2023-05-22 [1] Bioconductor
 biomaRt                2.56.1     2023-06-11 [1] Bioconductor
 Biostrings             2.68.1     2023-05-16 [1] Bioconductor
 bit                    4.0.5      2022-11-15 [1] CRAN (R 4.3.1)
 bit64                  4.0.5      2020-08-30 [1] CRAN (R 4.3.1)
 bitops                 1.0-7      2021-04-24 [1] CRAN (R 4.3.0)
 blob                   1.2.4      2023-03-17 [1] CRAN (R 4.3.1)
 cachem                 1.0.8      2023-05-01 [1] CRAN (R 4.3.1)
 callr                  3.7.3      2022-11-02 [1] CRAN (R 4.3.1)
 cli                    3.6.1      2023-03-23 [1] CRAN (R 4.3.1)
 codetools              0.2-19     2023-02-01 [2] CRAN (R 4.3.1)
 colorspace             2.1-0      2023-01-23 [1] CRAN (R 4.3.1)
 crayon                 1.5.2      2022-09-29 [1] CRAN (R 4.3.1)
 curl                   5.0.1      2023-06-07 [1] CRAN (R 4.3.1)
 data.table             1.14.8     2023-02-17 [1] CRAN (R 4.3.2)
 DBI                    1.1.3      2022-06-18 [1] CRAN (R 4.3.1)
 dbplyr                 2.3.3      2023-07-07 [1] CRAN (R 4.3.1)
 DelayedArray           0.26.7     2023-07-28 [1] Bioconductor
 DESeq2                 1.40.2     2023-06-25 [1] Bioconductor
 devtools               2.4.5      2022-10-11 [1] CRAN (R 4.3.2)
 digest                 0.6.33     2023-07-07 [1] CRAN (R 4.3.1)
 downloader             0.4        2015-07-09 [1] CRAN (R 4.3.2)
 dplyr                  1.1.3      2023-09-03 [1] CRAN (R 4.3.2)
 easyTCGA             * 0.0.1.8000 2023-11-06 [1] Github (ayueme/easyTCGA@0663870)
 edgeR                  3.42.4     2023-06-01 [1] Bioconductor
 ellipsis               0.3.2      2021-04-29 [1] CRAN (R 4.3.1)
 evaluate               0.21       2023-05-05 [1] CRAN (R 4.3.1)
 fansi                  1.0.4      2023-01-22 [1] CRAN (R 4.3.1)
 fastmap                1.1.1      2023-02-24 [1] CRAN (R 4.3.1)
 filelock               1.0.2      2018-10-05 [1] CRAN (R 4.3.1)
 fs                     1.6.3      2023-07-20 [1] CRAN (R 4.3.1)
 generics               0.1.3      2022-07-05 [1] CRAN (R 4.3.1)
 GenomeInfoDb           1.36.4     2023-10-02 [1] Bioconductor
 GenomeInfoDbData       1.2.10     2023-10-18 [1] Bioconductor
 GenomicRanges          1.52.1     2023-10-08 [1] Bioconductor
 ggplot2                3.4.4      2023-10-12 [1] CRAN (R 4.3.2)
 glue                   1.6.2      2022-02-24 [1] CRAN (R 4.3.1)
 gtable                 0.3.3      2023-03-21 [1] CRAN (R 4.3.1)
 hms                    1.1.3      2023-03-21 [1] CRAN (R 4.3.1)
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 [1] C:/Users/Han Wang/AppData/Local/R/win-library/4.3
 [2] C:/Program Files/R/R-4.3.1/library

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