Matching transcriptomic data to clinical data
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11 months ago
Azra ▴ 10

Hello everyone,

I'm new to the R language and I need some help.

I have downloaded the transcriptomic data related to the "TCGA-GBM" by using the package TCGAbiolinks, and I've also downloaded the clinical data (XML files), knowing that I'm interested in clinical_radiation.

What I want to do is for example combine the transcriptomic data to the clinical radiation for example.

Can anyone help me please? I'm really stuck.

Thanks in advance for your replies.

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What do you mean by "combine"? Please show us the code you used to get your datasets.

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query_GBM2 <- GDCquery(project = "TCGA-GBM",
  data.category = "Transcriptome Profiling", 
  data.type = "Gene Expression Quantification",
  workflow.type="STAR - Counts")

GDCdownload(query_GBM2) data1<- GDCprepare(query_GBM2, save = TRUE, save.filename = "data1.rda")

GBMMatrice <- assay(data1,"tpm_unstrand")

Rnaseq_CorOutliers <- TCGAanalyze_Preprocessing(data1) 
dataNorm1 <- TCGAanalyze_Normalization(tabDF = data1, geneInfo = geneInfoHT) 
dataFilt1 <- TCGAanalyze_Filtering(tabDF = dataNorm1, method = "quantile", qnt.cut = 0.25) samplesNT1 <- TCGAquery_SampleTypes(barcode = colnames(dataFilt1), c("NT"))
samplesTP1 <- TCGAquery_SampleTypes(barcode = colnames(dataFilt1), c("TP")) 
dataDEGs1 <- TCGAanalyze_DEA(mat1 = dataFilt1[,samplesNT1], mat2 = dataFilt1[,samplesTP1], Cond1type = "Normal", Cond2type = "Tumor", fdr.cut = 0.01 , logFC.cut = 1, method = "glmLRT") dataDEGsFiltLevel1 <- TCGAanalyze_LevelTab(dataDEGs1,"Tumor","Normal", dataFilt1[,samplesTP1],dataFilt1[,samplesNT1]) 
query_GBM<- GDCquery( project = "TCGA-GBM", data.category = "Clinical", data.type = "Clinical Supplement", data.format = "BCR Biotab" ) 
GDCdownload(query_GBM) clinical.BCRtab.all <- GDCprepare(query_GBM) names(clinical.BCRtab.all) 
clinical.BCRtab.all$clinical_radiation_gbm %>% head %>% DT::datatable(options = list(scrollX = TRUE, keys = TRUE))

This is the code that I used. What I am trying to do is actually a transcriptomic analysis and retrieve the DEGs. After that, I have tried to combine the transcriptomic file (which contains the samples of patients and the genes) to the clinical data (especially the clinical radiation) and this is where I got stuck. As I said, I'm not familiar with R so I don't know if my procedure is right or not. Thank you for your reply.

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Where did you get this code from? You'll probably just need a join of some sort to merge the clinical and transcriptomic data.

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I got it from the script of this topic: "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages". It's the work of Tiago Chedraoui Silva and al. The fact is I don't know how I could merge the data. I think that what the two datasets have in common is the BCR_patient_barcode, but I don't know which function I could use...

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That helps, thanks. What is the output to:

head(GBMMatrice)
head(clinical.BCRtab.all$clinical_radiation_gbm)
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enter image description here

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Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

code_formatting

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Ah, thank you, I didn't know. Here is the link for the GitHub Gist:

head(GBMMatrice)
TCGA-06-5410-01A-01R-1849-01 TCGA-19-5960-01A-11R-1850-01
ENSG00000000003.15 30.2938 110.8961
ENSG00000000005.6 0.1268 1.1017
ENSG00000000419.13 77.9820 108.3149
ENSG00000000457.14 4.3317 9.8632
ENSG00000000460.17 3.7300 8.0895
TCGA-14-0781-01B-01R-1849-01 TCGA-19-4065-02A-11R-2005-01
ENSG00000000003.15 64.7367 45.6468
ENSG00000000005.6 0.1240 0.1570
ENSG00000000419.13 61.1877 68.6560
ENSG00000000457.14 3.7656 4.1403
ENSG00000000460.17 3.1055 2.4838
TCGA-02-2483-01A-01R-1849-01 TCGA-06-2570-01A-01R-1849-01
ENSG00000000003.15 68.4328 75.8634
ENSG00000000005.6 0.0868 0.4239
ENSG00000000419.13 130.2599 69.6552
ENSG00000000457.14 5.2591 7.2493
ENSG00000000460.17 4.5610 5.6462
TCGA-06-2563-01A-01R-1849-01 TCGA-76-4929-01A-01R-1850-01
ENSG00000000003.15 93.2578 117.6090
ENSG00000000005.6 0.6305 5.6656
ENSG00000000419.13 107.1737 90.8538
ENSG00000000457.14 6.4285 7.6404
ENSG00000000460.17 5.4135 2.3827
TCGA-06-5858-01A-01R-1849-01 TCGA-06-2559-01A-01R-1849-01
ENSG00000000003.15 128.4459 69.5439
ENSG00000000005.6 7.0286 0.4599
ENSG00000000419.13 84.6279 112.2372
ENSG00000000457.14 5.7158 8.4532
ENSG00000000460.17 5.8681 8.4303
TCGA-28-5218-01A-01R-1850-01 TCGA-27-1832-01A-01R-1850-01
ENSG00000000003.15 76.9722 110.4830
ENSG00000000005.6 212.6327 5.0496
ENSG00000000419.13 85.4885 73.6915
ENSG00000000457.14 8.0810 6.2196
ENSG00000000460.17 4.7098 5.1485
TCGA-28-5207-01A-01R-1850-01 TCGA-06-0743-01A-01R-1849-01
ENSG00000000003.15 85.0811 55.9218
ENSG00000000005.6 4.4669 4.4077
ENSG00000000419.13 99.5538 77.4013
ENSG00000000457.14 8.7423 3.7713
ENSG00000000460.17 4.0131 2.5500
TCGA-76-4928-01B-01R-1850-01 TCGA-12-1597-01B-01R-1849-01
ENSG00000000003.15 66.0662 65.4497
ENSG00000000005.6 0.2063 0.1300
ENSG00000000419.13 89.2847 116.4637
ENSG00000000457.14 4.2106 5.1580
ENSG00000000460.17 3.8754 4.5968
TCGA-08-0386-01A-01R-1849-01 TCGA-19-2620-01A-01R-1850-01
ENSG00000000003.15 60.2725 65.7113
ENSG00000000005.6 0.9876 0.1568
ENSG00000000419.13 73.9374 48.6224
ENSG00000000457.14 7.3182 4.4398
ENSG00000000460.17 5.2496 2.0359
TCGA-06-0745-01A-01R-1849-01 TCGA-15-1444-01A-02R-1850-01
ENSG00000000003.15 53.9190 79.3015
ENSG00000000005.6 0.4811 0.6253
ENSG00000000419.13 124.8737 61.3413
ENSG00000000457.14 4.0838 5.4407
ENSG00000000460.17 5.2139 5.1131
TCGA-14-1823-01A-01R-1849-01 TCGA-02-0055-01A-01R-1849-01
ENSG00000000003.15 177.3700 49.6363
ENSG00000000005.6 2.9824 43.5238
ENSG00000000419.13 104.5023 155.8699
ENSG00000000457.14 5.3747 4.8667
ENSG00000000460.17 4.9346 4.2146
TCGA-32-2616-01A-01R-1850-01 TCGA-06-0129-01A-01R-1849-01
ENSG00000000003.15 52.0545 72.2196
ENSG00000000005.6 1.0370 0.2503
ENSG00000000419.13 74.9627 87.9180
ENSG00000000457.14 4.3020 9.8774
ENSG00000000460.17 4.2795 10.3977
TCGA-06-0132-01A-02R-1849-01 TCGA-19-1390-01A-01R-1850-01
ENSG00000000003.15 24.9750 21.6593
ENSG00000000005.6 0.5043 0.0472
ENSG00000000419.13 46.6486 58.7679
ENSG00000000457.14 2.8021 6.2764
ENSG00000000460.17 3.0720 6.9562
TCGA-06-0747-01A-01R-1849-01 TCGA-06-5411-01A-01R-1849-01
ENSG00000000003.15 67.1411 31.9528
ENSG00000000005.6 0.0495 0.3769
ENSG00000000419.13 102.9995 94.3751
ENSG00000000457.14 5.3411 5.4417
ENSG00000000460.17 3.8563 3.5200
TCGA-06-5859-01A-01R-1849-01 TCGA-19-2624-01A-01R-1850-01
ENSG00000000003.15 106.8657 57.5974
ENSG00000000005.6 6.5304 0.5192
ENSG00000000419.13 96.0231 74.9802
ENSG00000000457.14 10.8756 8.2191
ENSG00000000460.17 6.0676 5.8700
TCGA-26-5136-01B-01R-1850-01 TCGA-02-0047-01A-01R-1849-01
ENSG00000000003.15 65.4563 50.9506
ENSG00000000005.6 1.4938 0.1954
ENSG00000000419.13 75.3496 52.8074
ENSG00000000457.14 4.3510 4.9584
ENSG00000000460.17 3.4469 3.4783
TCGA-06-0168-01A-01R-1849-01 TCGA-06-0156-01A-02R-1849-01
ENSG00000000003.15 54.7729 61.3677
ENSG00000000005.6 0.1870 0.8593
ENSG00000000419.13 42.7691 83.4367
ENSG00000000457.14 4.2914 6.6339
ENSG00000000460.17 5.0402 7.2377
TCGA-28-2499-01A-01R-1850-01 TCGA-76-4931-01A-01R-1850-01
ENSG00000000003.15 178.1864 71.2790
ENSG00000000005.6 0.3367 0.2270
ENSG00000000419.13 71.0517 84.3173
ENSG00000000457.14 4.1566 6.6323
ENSG00000000460.17 2.2713 5.9630
TCGA-06-5413-01A-01R-1849-01 TCGA-27-1835-01A-01R-1850-01
ENSG00000000003.15 146.2413 50.5620
ENSG00000000005.6 2.0149 0.2301
ENSG00000000419.13 132.6740 75.2043
ENSG00000000457.14 7.6998 5.1937
ENSG00000000460.17 7.6639 2.6597
TCGA-76-4927-01A-01R-1850-01 TCGA-26-5133-01A-01R-1850-01
ENSG00000000003.15 74.8750 83.1525
ENSG00000000005.6 0.2551 0.1124
ENSG00000000419.13 64.4713 96.9452
ENSG00000000457.14 5.4887 5.6065
ENSG00000000460.17 4.6042 4.2397
TCGA-19-0957-02A-11R-2005-01 TCGA-28-2509-01A-01R-1850-01
ENSG00000000003.15 34.2730 60.1455
ENSG00000000005.6 0.2051 0.6256
ENSG00000000419.13 46.9677 121.7787
ENSG00000000457.14 4.9373 6.4029
ENSG00000000460.17 2.9793 7.1008
TCGA-27-1837-01A-01R-1850-01 TCGA-06-2565-01A-01R-1849-01
ENSG00000000003.15 55.7864 104.1422
ENSG00000000005.6 0.2266 0.6745
ENSG00000000419.13 46.8351 117.6735
ENSG00000000457.14 3.9607 8.9074
ENSG00000000460.17 3.8941 5.1278
TCGA-06-2558-01A-01R-1849-01 TCGA-06-2561-01A-02R-1849-01
ENSG00000000003.15 75.3098 40.8302
ENSG00000000005.6 0.7184 0.2112
ENSG00000000419.13 92.9209 68.6202
ENSG00000000457.14 6.7430 5.7166
ENSG00000000460.17 6.3533 2.7408
TCGA-06-0749-01A-01R-1849-01 TCGA-14-1825-01A-01R-1850-01
ENSG00000000003.15 51.9519 70.3354
ENSG00000000005.6 2.8619 0.7486
ENSG00000000419.13 53.2419 95.2031
ENSG00000000457.14 3.8030 5.0165
ENSG00000000460.17 1.2875 5.4597
TCGA-19-2629-01A-01R-1850-01 TCGA-32-5222-01A-01R-1850-01
ENSG00000000003.15 51.3946 105.1259
ENSG00000000005.6 0.0952 0.3746
ENSG00000000419.13 61.8017 143.1418
ENSG00000000457.14 5.4392 7.0083
ENSG00000000460.17 4.3062 7.2234
TCGA-12-0821-01A-01R-1849-01 TCGA-27-1831-01A-01R-1850-01
ENSG00000000003.15 102.2279 128.5592
ENSG00000000005.6 3.2720 1.3449
ENSG00000000419.13 119.5844 109.0662
ENSG00000000457.14 6.5751 4.2866
ENSG00000000460.17 5.6235 3.4912
TCGA-12-0616-01A-01R-1849-01 TCGA-06-0238-01A-02R-1849-01
ENSG00000000003.15 71.5838 66.2069
ENSG00000000005.6 0.1507 0.0857
ENSG00000000419.13 105.4320 83.8446
ENSG00000000457.14 5.5272 5.0143
ENSG00000000460.17 6.1675 4.8070
TCGA-06-5856-01A-01R-1849-01 TCGA-12-0618-01A-01R-1849-01
ENSG00000000003.15 81.7144 65.4239
ENSG00000000005.6 0.9704 0.1890
ENSG00000000419.13 117.8779 74.3497
ENSG00000000457.14 7.3990 6.2505
ENSG00000000460.17 5.3183 6.1436
TCGA-06-0152-02A-01R-2005-01 TCGA-19-2625-01A-01R-1850-01
ENSG00000000003.15 50.9843 48.0085
ENSG00000000005.6 0.1591 0.7468
ENSG00000000419.13 98.1366 55.9626
ENSG00000000457.14 6.3809 5.4718
ENSG00000000460.17 5.7963 3.6518
TCGA-06-5414-01A-01R-1849-01 TCGA-06-5417-01A-01R-1849-01
ENSG00000000003.15 81.0555 93.6448
ENSG00000000005.6 0.1421 0.0000
ENSG00000000419.13 107.2344 118.3314
ENSG00000000457.14 6.5019 13.9968
ENSG00000000460.17 5.2473 5.9246
TCGA-76-4926-01B-01R-1850-01 TCGA-28-5220-01A-01R-1850-01
ENSG00000000003.15 113.3587 129.5973
ENSG00000000005.6 2.5210 1.5586
ENSG00000000419.13 68.5659 123.5460
ENSG00000000457.14 6.4974 7.6036
ENSG00000000460.17 3.9360 4.3351
TCGA-19-4065-01A-01R-2005-01 TCGA-27-2524-01A-01R-1850-01
ENSG00000000003.15 63.8555 58.2440
ENSG00000000005.6 0.0405 0.1021
ENSG00000000419.13 120.6315 94.7089
ENSG00000000457.14 6.1731 3.6895
ENSG00000000460.17 4.9219 4.9353
TCGA-14-2554-01A-01R-1850-01 TCGA-28-5216-01A-01R-1850-01
ENSG00000000003.15 337.4063 48.3415
ENSG00000000005.6 14.7159 0.8126
ENSG00000000419.13 114.8951 88.8484
ENSG00000000457.14 5.1786 5.6194
ENSG00000000460.17 4.3380 4.4196
TCGA-28-1753-01A-01R-1850-01 TCGA-27-2528-01A-01R-1850-01
ENSG00000000003.15 47.1809 92.3314
ENSG00000000005.6 0.1111 0.2575
ENSG00000000419.13 67.6630 121.8554
ENSG00000000457.14 4.9320 4.6823
ENSG00000000460.17 3.8458 5.1692
TCGA-32-1982-01A-01R-1850-01 TCGA-14-1402-02A-01R-2005-01
ENSG00000000003.15 105.1941 137.9040
ENSG00000000005.6 0.1458 1.1640
ENSG00000000419.13 68.2644 190.8045
ENSG00000000457.14 5.3447 5.5038
ENSG00000000460.17 3.4594 7.4822
TCGA-12-5295-01A-01R-1849-01 TCGA-76-4932-01A-01R-1850-01
ENSG00000000003.15 97.2991 92.9495
ENSG00000000005.6 0.3689 0.3167
ENSG00000000419.13 121.4097 66.3511
ENSG00000000457.14 4.2976 7.0174
ENSG00000000460.17 5.5780 5.1545
TCGA-26-5139-01A-01R-1850-01 TCGA-06-2562-01A-01R-1849-01
ENSG00000000003.15 99.7715 78.8837
ENSG00000000005.6 0.4185 0.0993
ENSG00000000419.13 76.9782 124.2398
ENSG00000000457.14 5.7047 6.1122
ENSG00000000460.17 3.5767 4.4074
TCGA-06-0157-01A-01R-1849-01 TCGA-06-5412-01A-01R-1849-01
ENSG00000000003.15 114.9393 90.7013
ENSG00000000005.6 0.2543 0.0925
ENSG00000000419.13 71.1522 80.6087
ENSG00000000457.14 5.1698 4.3814
ENSG00000000460.17 5.7089 3.6800
TCGA-06-0646-01A-01R-1849-01 TCGA-06-0174-01A-01R-1849-01
ENSG00000000003.15 44.6427 81.2876
ENSG00000000005.6 0.6921 0.1187
ENSG00000000419.13 56.5095 72.6344
ENSG00000000457.14 6.7814 6.1586
ENSG00000000460.17 5.8309 6.8217
TCGA-15-0742-01A-01R-1850-01 TCGA-06-0645-01A-01R-1849-01
ENSG00000000003.15 72.5375 44.1409
ENSG00000000005.6 0.5169 0.5011
ENSG00000000419.13 100.1794 77.8868
ENSG00000000457.14 3.9014 4.8894
ENSG00000000460.17 3.1946 4.2000
TCGA-14-0790-01B-01R-1849-01 TCGA-06-2564-01A-01R-1849-01
ENSG00000000003.15 93.3216 82.0863
ENSG00000000005.6 0.7912 0.8718
ENSG00000000419.13 76.4306 82.3426
ENSG00000000457.14 5.4969 7.7312
ENSG00000000460.17 3.8925 5.3506
TCGA-06-0678-11A-32R-A36H-07 TCGA-06-0878-01A-01R-1849-01
ENSG00000000003.15 7.3646 61.4441
ENSG00000000005.6 0.2504 1.8355
ENSG00000000419.13 56.8229 90.4849
ENSG00000000457.14 4.3165 5.7565
ENSG00000000460.17 0.7552 4.3395
TCGA-14-0787-01A-01R-1849-01 TCGA-06-5408-01A-01R-1849-01
ENSG00000000003.15 67.6905 55.6232
ENSG00000000005.6 0.2430 0.7469
ENSG00000000419.13 135.2169 102.8219
ENSG00000000457.14 4.8813 7.9285
ENSG00000000460.17 4.4862 4.2342
TCGA-06-0158-01A-01R-1849-01 TCGA-41-5651-01A-01R-1850-01
ENSG00000000003.15 98.1647 62.3738
ENSG00000000005.6 0.6515 0.3449
ENSG00000000419.13 74.0885 118.7632
ENSG00000000457.14 6.0501 9.4073
ENSG00000000460.17 5.5010 6.9749
TCGA-14-0736-02A-01R-2005-01 TCGA-06-0686-01A-01R-1849-01
ENSG00000000003.15 98.0397 52.4703
ENSG00000000005.6 2.4166 0.1030
ENSG00000000419.13 77.4430 57.8333
ENSG00000000457.14 3.8257 4.5516
ENSG00000000460.17 2.1614 4.5853
TCGA-28-5215-01A-01R-1850-01 TCGA-32-1980-01A-01R-1850-01
ENSG00000000003.15 68.6205 24.3036
ENSG00000000005.6 0.9312 0.4089
ENSG00000000419.13 84.5021 74.3346
ENSG00000000457.14 5.8327 5.0076
ENSG00000000460.17 6.2522 3.2461
TCGA-06-0178-01A-01R-1849-01 TCGA-26-1442-01A-01R-1850-01
ENSG00000000003.15 87.7843 46.3122
ENSG00000000005.6 0.3052 0.2254
ENSG00000000419.13 89.9389 43.3160
ENSG00000000457.14 7.5259 3.7617
ENSG00000000460.17 8.4002 1.9317
TCGA-06-0138-01A-02R-1849-01 TCGA-06-0156-01A-03R-1849-01
ENSG00000000003.15 93.3645 70.8772
ENSG00000000005.6 1.6895 0.6612
ENSG00000000419.13 100.7507 100.4669
ENSG00000000457.14 4.9875 6.9597
ENSG00000000460.17 4.8174 8.1058
TCGA-27-2523-01A-01R-1850-01 TCGA-41-2572-01A-01R-1850-01
ENSG00000000003.15 75.0558 65.4922
ENSG00000000005.6 0.2584 0.5120
ENSG00000000419.13 122.6455 81.0445
ENSG00000000457.14 5.1635 3.1962
ENSG00000000460.17 7.3584 3.2911
TCGA-14-1034-01A-01R-1849-01 TCGA-06-0210-01A-01R-1849-01
ENSG00000000003.15 96.0510 81.7969
ENSG00000000005.6 0.3029 0.1334
ENSG00000000419.13 68.5263 80.0162
ENSG00000000457.14 3.0529 4.8043
ENSG00000000460.17 3.5947 2.8904
TCGA-06-0211-01A-01R-1849-01 TCGA-06-0130-01A-01R-1849-01
ENSG00000000003.15 71.2257 40.8655
ENSG00000000005.6 0.3862 0.1024
ENSG00000000419.13 85.0854 108.0601
ENSG00000000457.14 5.4429 5.2918
ENSG00000000460.17 6.2343 5.8099
TCGA-06-0139-01A-01R-1849-01 TCGA-06-0744-01A-01R-1849-01
ENSG00000000003.15 38.2822 60.4576
ENSG00000000005.6 0.3028 0.3522
ENSG00000000419.13 80.9140 72.5223
ENSG00000000457.14 4.2535 4.7773
ENSG00000000460.17 4.9414 2.6995
TCGA-06-0125-01A-01R-1849-01 TCGA-06-2557-01A-01R-1849-01
ENSG00000000003.15 76.7833 50.0850
ENSG00000000005.6 0.4035 0.7806
ENSG00000000419.13 97.4399 82.3758
ENSG00000000457.14 6.5428 6.5974
ENSG00000000460.17 5.9849 7.7653
TCGA-28-2514-01A-02R-1850-01 TCGA-28-5208-01A-01R-1850-01
ENSG00000000003.15 59.2722 116.3035
ENSG00000000005.6 0.4423 0.3766
ENSG00000000419.13 69.0219 107.4275
ENSG00000000457.14 6.5082 6.5986
ENSG00000000460.17 4.9340 8.4324
TCGA-41-3915-01A-01R-1850-01 TCGA-12-5299-01A-02R-1849-01
ENSG00000000003.15 83.7328 91.2634
ENSG00000000005.6 0.6247 0.5391
ENSG00000000419.13 69.1825 89.1148
ENSG00000000457.14 5.6714 6.1584
ENSG00000000460.17 5.3546 4.4588
TCGA-06-5418-01A-01R-1849-01 TCGA-16-0846-01A-01R-1850-01
ENSG00000000003.15 84.0034 43.9793
ENSG00000000005.6 0.8864 0.1093
ENSG00000000419.13 105.1454 66.7390
ENSG00000000457.14 4.8304 4.1823
ENSG00000000460.17 3.8546 2.8904
TCGA-14-0817-01A-01R-1849-01 TCGA-06-2567-01A-01R-1849-01
ENSG00000000003.15 111.6119 67.2886
ENSG00000000005.6 4.0701 0.6697
ENSG00000000419.13 106.3794 73.8971
ENSG00000000457.14 7.5290 7.4128
ENSG00000000460.17 7.4972 7.5530
TCGA-06-0649-01B-01R-1849-01 TCGA-06-0681-11A-41R-A36H-07
ENSG00000000003.15 79.3682 7.6565
ENSG00000000005.6 0.6525 0.3879
ENSG00000000419.13 64.8938 56.5988
ENSG00000000457.14 3.9409 4.4173
ENSG00000000460.17 3.1725 1.0761
TCGA-06-0882-01A-01R-1849-01 TCGA-32-4213-01A-01R-1850-01
ENSG00000000003.15 57.2746 73.0126
ENSG00000000005.6 0.5082 0.2325
ENSG00000000419.13 92.0853 62.2702
ENSG00000000457.14 5.6865 2.6925
ENSG00000000460.17 2.9126 3.0756
TCGA-06-0680-11A-32R-A36H-07 TCGA-27-2521-01A-01R-1850-01
ENSG00000000003.15 9.6966 5.8836
ENSG00000000005.6 0.2132 1.3023
ENSG00000000419.13 50.6207 115.9459
ENSG00000000457.14 5.5400 6.9493
ENSG00000000460.17 0.8537 4.3589
TCGA-32-2632-01A-01R-1850-01 TCGA-02-2485-01A-01R-1849-01
ENSG00000000003.15 60.1680 96.8388
ENSG00000000005.6 0.5932 0.2957
ENSG00000000419.13 70.6241 84.0390
ENSG00000000457.14 4.1629 7.0134
ENSG00000000460.17 4.8529 7.6327
TCGA-06-2569-01A-01R-1849-01 TCGA-06-AABW-11A-31R-A36H-07
ENSG00000000003.15 129.0445 8.2985
ENSG00000000005.6 112.6043 0.0000
ENSG00000000419.13 134.7626 60.0317
ENSG00000000457.14 12.2243 7.0446
ENSG00000000460.17 14.0648 2.2289
TCGA-32-2615-01A-01R-1850-01 TCGA-28-2513-01A-01R-1850-01
ENSG00000000003.15 88.0703 60.1498
ENSG00000000005.6 1.2721 0.0555
ENSG00000000419.13 88.2958 83.7239
ENSG00000000457.14 5.8886 4.3105
ENSG00000000460.17 3.5790 4.4068
TCGA-06-0219-01A-01R-1849-01 TCGA-28-5204-01A-01R-1850-01
ENSG00000000003.15 82.4402 97.0937
ENSG00000000005.6 0.0865 0.1846
ENSG00000000419.13 107.5209 110.9704
ENSG00000000457.14 5.5554 7.0847
ENSG00000000460.17 5.4854 6.5102
TCGA-19-1389-02A-21R-2005-01 TCGA-12-3653-01A-01R-1849-01
ENSG00000000003.15 56.1192 170.5745
ENSG00000000005.6 0.0000 0.8915
ENSG00000000419.13 75.4281 84.7078
ENSG00000000457.14 3.8505 6.5382
ENSG00000000460.17 2.5348 7.2295
TCGA-19-1787-01B-01R-1850-01 TCGA-06-5416-01A-01R-1849-01
ENSG00000000003.15 56.7117 47.9463
ENSG00000000005.6 12.3961 0.0753
ENSG00000000419.13 78.7723 129.9806
ENSG00000000457.14 3.4044 6.5585
ENSG00000000460.17 6.3446 7.1891
TCGA-06-0141-01A-01R-1849-01 TCGA-12-3650-01A-01R-1849-01
ENSG00000000003.15 37.0664 78.7707
ENSG00000000005.6 0.0976 0.6426
ENSG00000000419.13 71.8164 68.0289
ENSG00000000457.14 3.6191 5.2954
ENSG00000000460.17 2.1788 8.5338
TCGA-26-5135-01A-01R-1850-01 TCGA-14-0871-01A-01R-1849-01
ENSG00000000003.15 44.7739 167.9793
ENSG00000000005.6 0.2673 156.8253
ENSG00000000419.13 59.6564 151.2862
ENSG00000000457.14 4.7004 4.1957
ENSG00000000460.17 3.4531 12.8003
TCGA-27-1834-01A-01R-1850-01 TCGA-06-5415-01A-01R-1849-01
ENSG00000000003.15 106.5189 95.7581
ENSG00000000005.6 1.5648 0.8233
ENSG00000000419.13 75.1449 117.6062
ENSG00000000457.14 5.4465 7.4290
ENSG00000000460.17 3.7349 5.2377
TCGA-06-0190-02A-01R-2005-01 TCGA-27-1830-01A-01R-1850-01
ENSG00000000003.15 40.8241 70.7455
ENSG00000000005.6 1.1342 0.5954
ENSG00000000419.13 85.4610 73.9292
ENSG00000000457.14 4.0998 6.2558
ENSG00000000460.17 5.4879 3.7066
TCGA-41-4097-01A-01R-1850-01 TCGA-32-1970-01A-01R-1850-01
ENSG00000000003.15 46.4405 60.4303
ENSG00000000005.6 0.0770 0.8658
ENSG00000000419.13 61.8469 52.6728
ENSG00000000457.14 5.2659 5.6279
ENSG00000000460.17 2.6074 4.0002
TCGA-06-0190-01A-01R-1849-01 TCGA-41-2571-01A-01R-1850-01
ENSG00000000003.15 70.0066 30.2841
ENSG00000000005.6 0.2893 0.1136
ENSG00000000419.13 80.6678 92.6183
ENSG00000000457.14 4.8642 5.8728
ENSG00000000460.17 6.9529 4.1862
TCGA-28-2510-01A-01R-1850-01 TCGA-06-0644-01A-02R-1849-01
ENSG00000000003.15 19.8911 60.0428
ENSG00000000005.6 0.5698 0.0495
ENSG00000000419.13 60.6253 99.3058
ENSG00000000457.14 4.6435 4.0619
ENSG00000000460.17 2.2542 5.4779
TCGA-28-5213-01A-01R-1850-01 TCGA-02-2486-01A-01R-1849-01
ENSG00000000003.15 132.2837 111.9005
ENSG00000000005.6 6.8109 0.5794
ENSG00000000419.13 126.8432 102.5288
ENSG00000000457.14 5.4590 5.9393
ENSG00000000460.17 4.1131 3.0513
TCGA-14-0789-01A-01R-1849-01 TCGA-06-0211-01B-01R-1849-01
ENSG00000000003.15 56.4860 94.2605
ENSG00000000005.6 0.0665 0.2525
ENSG00000000419.13 50.5503 94.5335
ENSG00000000457.14 4.7743 6.9190
ENSG00000000460.17 2.4647 8.3890
TCGA-06-0211-02A-02R-2005-01 TCGA-16-1045-01B-01R-1850-01
ENSG00000000003.15 68.5342 69.9159
ENSG00000000005.6 0.3854 1.1781
ENSG00000000419.13 119.5198 72.7503
ENSG00000000457.14 5.3726 5.4033
ENSG00000000460.17 4.5333 3.5113
TCGA-27-2526-01A-01R-1850-01 TCGA-06-0125-02A-11R-2005-01
ENSG00000000003.15 96.3848 82.9215
ENSG00000000005.6 1.7652 0.4189
ENSG00000000419.13 106.4524 63.4521
ENSG00000000457.14 3.1365 5.4929
ENSG00000000460.17 3.0051 3.1369
TCGA-19-2619-01A-01R-1850-01 TCGA-06-1804-01A-01R-1849-01
ENSG00000000003.15 81.9417 51.8153
ENSG00000000005.6 0.2421 0.3312
ENSG00000000419.13 70.4124 65.9500
ENSG00000000457.14 4.8601 5.1332
ENSG00000000460.17 3.2926 3.2281
TCGA-14-1829-01A-01R-1850-01 TCGA-06-0171-02A-11R-2005-01
ENSG00000000003.15 239.2504 30.1774
ENSG00000000005.6 7.0392 0.1364
ENSG00000000419.13 138.1743 55.5088
ENSG00000000457.14 5.0205 5.0426
ENSG00000000460.17 6.1234 2.7663
TCGA-06-0750-01A-01R-1849-01 TCGA-76-4925-01A-01R-1850-01
ENSG00000000003.15 60.9806 78.7018
ENSG00000000005.6 2.5421 0.4110
ENSG00000000419.13 74.5538 169.7759
ENSG00000000457.14 3.4238 6.7280
ENSG00000000460.17 1.7422 5.8939
TCGA-14-1034-02B-01R-2005-01 TCGA-06-0221-02A-11R-2005-01
ENSG00000000003.15 124.6713 34.3045
ENSG00000000005.6 0.6071 0.1278
ENSG00000000419.13 147.5142 65.3189
ENSG00000000457.14 8.8892 7.6179
ENSG00000000460.17 10.8276 6.8873
TCGA-32-2634-01A-01R-1850-01 TCGA-28-1747-01C-01R-1850-01
ENSG00000000003.15 97.4277 91.4360
ENSG00000000005.6 0.6688 0.4451
ENSG00000000419.13 133.6428 68.9969
ENSG00000000457.14 6.2915 5.5127
ENSG00000000460.17 7.7829 4.0721
TCGA-06-0210-02A-01R-2005-01 TCGA-06-0184-01A-01R-1849-01
ENSG00000000003.15 47.4205 90.9708
ENSG00000000005.6 0.5607 0.4192
ENSG00000000419.13 49.7091 67.9240
ENSG00000000457.14 4.8995 4.0992
ENSG00000000460.17 4.2395 2.8605
TCGA-06-0675-11A-32R-A36H-07 TCGA-12-0619-01A-01R-1849-01
ENSG00000000003.15 8.7417 44.7954
ENSG00000000005.6 0.3093 0.6426
ENSG00000000419.13 53.2762 74.7138
ENSG00000000457.14 4.6618 7.0874
ENSG00000000460.17 0.8849 6.2192
TCGA-28-5209-01A-01R-1850-01 TCGA-12-3652-01A-01R-1849-01
ENSG00000000003.15 82.1417 122.5849
ENSG00000000005.6 0.5437 0.3432
ENSG00000000419.13 83.4400 119.4728
ENSG00000000457.14 6.7389 3.4468
ENSG00000000460.17 6.4656 5.1336
TCGA-32-2638-01A-01R-1850-01 TCGA-26-5134-01A-01R-1850-01
ENSG00000000003.15 106.4214 41.1994
ENSG00000000005.6 1.6188 0.5004
ENSG00000000419.13 93.3104 46.7143
ENSG00000000457.14 6.1924 5.0796
ENSG00000000460.17 3.9699 4.7017
TCGA-26-5132-01A-01R-1850-01 TCGA-06-0187-01A-01R-1849-01
ENSG00000000003.15 71.9519 55.2986
ENSG00000000005.6 1.1969 1.8746
ENSG00000000419.13 84.2576 51.8722
ENSG00000000457.14 6.3164 4.8353
ENSG00000000460.17 5.5325 4.0387
TCGA-27-2519-01A-01R-1850-01
ENSG00000000003.15 73.9880
ENSG00000000005.6 1.3390
ENSG00000000419.13 94.3014
ENSG00000000457.14 4.6154
ENSG00000000460.17 2.8445
[ getOption("max.print") est atteint -- ligne 1 omise ]
> head(clinical.BCRtab.all$clinical_radiation_gbm)
# A tibble: 6 × 18
bcr_patient_uuid bcr_patient_barcode bcr_radiation_barcode bcr_radiation_uuid form_completion_date
<chr> <chr> <chr> <chr> <chr>
1 bcr_patient_uuid bcr_patient_barcode bcr_radiation_barcode bcr_radiation_uuid form_completion_date
2 CDE_ID: CDE_ID:2003301 CDE_ID: CDE_ID: CDE_ID:
3 30a1fe5e-5b12-472c-… TCGA-02-0001 TCGA-02-0001-R22174 7a9b5aaf-6d85-4ce… 2009-4-3
4 df3c1d61-79c1-43e9-… TCGA-02-0003 TCGA-02-0003-R22178 e192833b-6b21-458… 2009-4-2
5 3ac8f759-2df0-4ef5-… TCGA-02-0004 TCGA-02-0004-R22183 8029e9fe-0956-4a4… 2009-4-7
6 98714d95-b62e-4f34-… TCGA-02-0006 TCGA-02-0006-R22189 3bcc9ca0-54ce-493… 2009-3-30
# ℹ 13 more variables: radiation_therapy_type <chr>, radiation_therapy_site <chr>,
# radiation_total_dose <chr>, radiation_adjuvant_units <chr>,
# radiation_adjuvant_fractions_total <chr>, radiation_therapy_started_days_to <chr>,
# radiation_therapy_ongoing_indicator <chr>, radiation_therapy_ended_days_to <chr>,
# treatment_best_response <chr>, course_number <chr>, radiation_type_other <chr>,
# therapy_regimen <chr>, therapy_regimen_other <chr>
view raw gistfile1.txt hosted with ❤ by GitHub

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Nicely done. However, given that you have a ton of columns (which I did not know), maybe a better option would have been GBMMatrice[1:10,1:10]. In any case, please use gists/direct copy-paste in the future, it makes things a lot easier than screenshots

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Thanks for the advice! I'll keep that in mind for next time.

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enter image description here

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Thank you for your help. For the head (GBMMatrice), I have multiple samples not only the ones that are on the screenshot, but it's always with the same rows of genes.

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Use a SummarizedExperiment object - that will work best for you. With some digging, you'll be able to figure out how to place both pieces of information in the same SummarizedExperiment object.

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Do you mean using this function like below? SummarizedExperiment(GBMMatrice) SummarizedExperiment(clinical.radiation)

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No - please do some digging. The RNA data will be the assay and clinical metadata will become colData (I think, I'm not sure I got the keyword right). There is very minimal work required, I want you to put the effort in instead of asking around.

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Thank you for your help . I'll keep digging.

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I tried something else. I used the package TCGAutils to convert the file-id to the corresponding TCGAbarcode of the patients. Now, I'll try to use a function to merge the two datasets.

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Try everything and post the solution that works for you as an answer. You are so close to cracking this!

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