title: "TCGA PRAD" author: "Levi Waldron" date: "September 14, 2015" output: html_document
Load TCGA data
if(!require(RTCGAToolbox)){
biocLite("devtools")
biocLite(c("limma", "RCircos", "data.table", "RCurl", "RJSONIO"))
biocLite("Link-NY/RTCGAToolbox")
}## Warning: replacing previous import by 'IRanges::shift' when loading
## 'RTCGAToolbox'library(DESeq2)Download TCGA PRAD data
library(RTCGAToolbox)
rundates <- getFirehoseRunningDates()
analysisdates <- getFirehoseAnalyzeDates()
prad <- getFirehoseData("PRAD", runDate=rundates[1],
gistic2_Date=analysisdates[1], RNAseq_Gene=TRUE,
miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP=TRUE,
CNV_SNP=TRUE, CNA_Seq=TRUE, CNA_CGH=TRUE, Methylation=TRUE,
Mutation=TRUE, mRNA_Array=TRUE, miRNA_Array=TRUE, RPPA=TRUE)## gdac.broadinstitute.org_PRAD.Clinical_Pick_Tier1.Level_4.2015040200.0.0.tar.gz
## Using locally cached version of ./20150402-PRAD-Clinical.txt
##
## gdac.broadinstitute.org_PRAD.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gz
## Using locally cached version of ./20150402-PRAD-RNAseq2GeneNorm.txt
## RNAseq2 data will be imported! This may take a while!
## Start: 2015-12-01 13:56:53##
Read 48.7% of 20533 rows
Read 97.4% of 20533 rows
Read 20533 rows and 551 (of 551) columns from 0.090 GB file in 00:00:06## Done: 2015-12-01 13:56:59
## gdac.broadinstitute.org_PRAD.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2015040200.0.0.tar.gz
## Using locally cached version of ./20150402-PRAD-miRNAseqGene.txt
## miRNAseq data will be imported! This may take a while!
## Start: 2015-12-01 13:57:16
## Done: 2015-12-01 13:57:16
## gdac.broadinstitute.org_PRAD.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg.Level_3.2015040200.0.0.tar.gz
## Using locally cached version of ./20150402-PRAD-CNASNPHg19.txt
## gdac.broadinstitute.org_PRAD.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.Level_3.2015040200.0.0.tar.gz
## Using locally cached version of ./20150402-PRAD-CNVSNPHg19.txt
## gdac.broadinstitute.org_PRAD.Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.Level_3.2015040200.0.0.tar.gz
## Using locally cached version of ./20150402-PRAD-CNAseq.txt
##
## gdac.broadinstitute.org_PRAD.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2015040200.0.0.tar.gz
## http://gdac.broadinstitute.org/runs/stddata__2015_04_02/data/PRAD/20150402/gdac.broadinstitute.org_PRAD.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2015040200.0.0.tar.gz
## File Size: ~2066MB
## File above won't be downloaded due to data size, RTCGAToolbox will skip this data!
##
##
##
##
##
## gdac.broadinstitute.org_PRAD.Mutation_Packager_Calls.Level_3.2015040200.0.0.tar.gz
## gdac.broadinstitute.org_PRAD-TP.CopyNumber_Gistic2.Level_4.2014101700.0.0.tar.gzExtract available data types
choices <- tolower(gsub("_", "", c("RNAseq_Gene", "miRNASeq_Gene",
"RNAseq2_Gene_Norm", "CNA_SNP", "CNV_SNP", "CNA_Seq",
"CNA_CGH", "Methylation", "Mutation", "mRNA_Array",
"miRNA_Array", "RPPA")))dses <- lapply(choices, function(choice) try(extract(prad, choice,
clinic=TRUE),
silent=TRUE))
names(dses) <- choices
dses## $rnaseqgene
## [1] "Error in extract(prad, choice, clinic = TRUE) : \n There is no data for that data type!\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in extract(prad, choice, clinic = TRUE): There is no data for that data type!>
##
## $mirnaseqgene
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 1046 features, 537 samples
## element names: exprs
## protocolData: none
## phenoData
## sampleNames: tcga-2a-a8vl-01 tcga-2a-a8vo-01 ... tcga-zg-a9ni-01
## (537 total)
## varLabels: vital_status days_to_death ... center (242 total)
## varMetadata: labelDescription
## featureData: none
## experimentData: use 'experimentData(object)'
## Annotation:
##
## $rnaseq2genenorm
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 20501 features, 540 samples
## element names: exprs
## protocolData: none
## phenoData
## sampleNames: tcga-2a-a8vl-01 tcga-2a-a8vo-01 ... tcga-zg-a9ni-01
## (540 total)
## varLabels: vital_status days_to_death ... center (242 total)
## varMetadata: labelDescription
## featureData: none
## experimentData: use 'experimentData(object)'
## Annotation:
##
## $cnasnp
## GRangesList object of length 1009:
## $tcga-2a-a8vl-01
## GRanges object with 377 ranges and 2 metadata columns:
## seqnames ranges strand | Num_Probes Segment_Mean
## <Rle> <IRanges> <Rle> | <numeric> <numeric>
## [1] chr1 [ 61735, 16153497] * | 8417 0.0192
## [2] chr1 [16153536, 16155010] * | 9 -1.3997
## [3] chr1 [16165661, 25583291] * | 5733 0.0271
## [4] chr1 [25583341, 25646986] * | 29 -1.7924
## [5] chr1 [25661501, 35091594] * | 4967 0.0196
## ... ... ... ... ... ... ...
## [373] chr22 [24401529, 51234455] * | 18918 0.0199
## [374] chr23 [ 168477, 34044373] * | 21155 0.0011
## [375] chr23 [34046553, 34070287] * | 23 -3.3231
## [376] chr23 [34073425, 155182354] * | 62721 0.0039
## [377] chr24 [ 2650438, 59018259] * | 8631 -0.8552
##
## ...
## <1008 more elements>
## -------
## seqinfo: 24 sequences from an unspecified genome; no seqlengths
##
## $cnvsnp
## GRangesList object of length 1003:
## $tcga-2a-a8vl-01
## GRanges object with 117 ranges and 2 metadata columns:
## seqnames ranges strand | Num_Probes Segment_Mean
## <Rle> <IRanges> <Rle> | <numeric> <numeric>
## [1] chr1 [ 3218610, 46599744] * | 22807 0.0218
## [2] chr1 [46601887, 53641875] * | 3572 -0.3873
## [3] chr1 [53641911, 58304399] * | 3399 0.0166
## [4] chr1 [58314187, 58497759] * | 168 -0.37
## [5] chr1 [58498264, 104381295] * | 28166 0.0157
## ... ... ... ... ... ... ...
## [113] chr21 [42827478, 42864812] * | 101 -0.8952
## [114] chr21 [42867190, 42872410] * | 26 -0.3935
## [115] chr21 [42875404, 47678774] * | 2367 0.0223
## [116] chr22 [17423930, 49331012] * | 16920 0.024
## [117] chr23 [ 3157107, 154905589] * | 63256 0.0041
##
## ...
## <1002 more elements>
## -------
## seqinfo: 23 sequences from an unspecified genome; no seqlengths
##
## $cnaseq
## GRangesList object of length 230:
## $tcga-ch-5741-01
## GRanges object with 88 ranges and 2 metadata columns:
## seqnames ranges strand | Num_Probes
## <Rle> <IRanges> <Rle> | <numeric>
## [1] chr1 [ 10208, 170998749] * | <NA>
## [2] chr1 [170998750, 171222653] * | <NA>
## [3] chr1 [171222654, 249240606] * | <NA>
## [4] chr2 [ 10001, 243189359] * | <NA>
## [5] chr3 [ 60174, 70581515] * | <NA>
## ... ... ... ... ... ...
## [84] chr23 [128529035, 128582748] * | <NA>
## [85] chr23 [128582749, 154930285] * | <NA>
## [86] chr24 [ 2649474, 6711879] * | <NA>
## [87] chr24 [ 6711880, 6813216] * | <NA>
## [88] chr24 [ 6813217, 28809960] * | <NA>
## Segment_Mean
## <numeric>
## [1] 0.0445519350183502
## [2] -0.719244299367207
## [3] 0.0416368338763181
## [4] 0.0400665363289484
## [5] 0.0357777450352256
## ... ...
## [84] -2.31507050198042
## [85] 0.0277920429090032
## [86] 0.0865462501641183
## [87] 0.952415386548219
## [88] 0.101459215941079
##
## ...
## <229 more elements>
## -------
## seqinfo: 24 sequences from an unspecified genome; no seqlengths
##
## $cnacgh
## [1] "Error in extract(prad, choice, clinic = TRUE) : \n There is no data for that data type!\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in extract(prad, choice, clinic = TRUE): There is no data for that data type!>
##
## $methylation
## [1] "Error in extract(prad, choice, clinic = TRUE) : \n There is no data for that data type!\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in extract(prad, choice, clinic = TRUE): There is no data for that data type!>
##
## $mutation
## GRangesList object of length 420:
## $tcga-2a-a8vl-01
## GRanges object with 39 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] chr10 [ 29775061, 29775061] +
## [2] chr2 [ 30480447, 30480447] +
## [3] chr8 [ 39495171, 39495171] +
## [4] chr1 [158262073, 158262073] +
## [5] chr8 [ 41519413, 41519413] +
## ... ... ... ...
## [35] chr3 [138739004, 138739004] +
## [36] chr20 [ 33440316, 33440316] +
## [37] chr20 [ 33324502, 33324502] +
## [38] chr3 [195713385, 195713386] +
## [39] chr5 [180708776, 180708777] +
##
## ...
## <419 more elements>
## -------
## seqinfo: 25 sequences from an unspecified genome; no seqlengths
##
## $mrnaarray
## [1] "Error in extract(prad, choice, clinic = TRUE) : \n There is no data for that data type!\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in extract(prad, choice, clinic = TRUE): There is no data for that data type!>
##
## $mirnaarray
## [1] "Error in extract(prad, choice, clinic = TRUE) : \n There is no data for that data type!\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in extract(prad, choice, clinic = TRUE): There is no data for that data type!>
##
## $rppa
## [1] "Error in extract(prad, choice, clinic = TRUE) : \n There is no data for that data type!\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in extract(prad, choice, clinic = TRUE): There is no data for that data type!>eset <- extract(prad, "rnaseq2genenorm")
write.csv(exprs(eset), file="prad_rnaseq.csv")
write.csv(pData(eset), file="prad_clinical.csv")
saveRDS(eset, file="prad_eset.rds")To load the eset again:
eset <- readRDS("prad_eset.rds")Make a histogram of PSA (KLK3) expression
hist(exprs(eset["KLK3", ]))
hist(log(exprs(eset["KLK3", ])))
See what clinical data are available by default:
summary(pData(eset))## vital_status days_to_death days_to_last_followup
## Length:540 Length:540 Length:540
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## primary_site_of_disease neoplasm_diseasestage pathology_T_stage
## Length:540 Length:540 Length:540
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## pathology_N_stage dcc_upload_date gender
## Length:540 Length:540 Length:540
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## date_of_initial_pathologic_diagnosis radiation_therapy
## Length:540 Length:540
## Class :character Class :character
## Mode :character Mode :character
##
##
##
##
## histological_type radiations_radiation_regimenindication
## Length:540 Length:540
## Class :character Class :character
## Mode :character Mode :character
##
##
##
##
## completeness_of_resection number_of_lymph_nodes gleason_score_combined
## Length:540 Length:540 Length:540
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## gleason_score_primary gleason_score_secondary gleason_score
## Length:540 Length:540 Length:540
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## psa_result_preop days_to_preop_psa psa_value
## Length:540 Length:540 Length:540
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## days_to_psa race ethnicity
## Length:540 Length:540 Length:540
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## batch_number admin.batch_number
## Length:540 184.61.0: 78
## Class :character 429.22.0: 68
## Mode :character 91.57.0 : 68
## 389.30.0: 45
## 370.32.0: 42
## 357.34.0: 30
## (Other) :209
## admin.bcr admin.day_of_dcc_upload
## nationwide children's hospital:540 12: 4
## 26:534
## 29: 2
##
##
##
##
## admin.file_uuid admin.month_of_dcc_upload
## 016de7f0-1048-4add-ba29-85ba6a4dc4f7: 2 1: 2
## 060644b7-7ff0-481a-9f83-fc23dc16df91: 2 2: 2
## 076d02bb-3504-4139-91b7-5d52883cb39a: 2 3:536
## 09cc76ff-9742-4af8-8c0f-2998a5561dfc: 2
## 0ad65f96-3ab3-491e-8a17-1844474e3886: 2
## 0bb87419-ce94-4a3a-94b9-ca797cca10b7: 2
## (Other) :528
## patient.additional_studies patient.age_at_initial_pathologic_diagnosis
## NA's:540 66 : 36
## 61 : 32
## 64 : 31
## 57 : 30
## 63 : 29
## 62 : 27
## (Other):355
## patient.bcr_patient_uuid
## 00e41e6a-9fe7-44f9-978b-7b05b179506a: 2
## 0730216b-c201-443c-9092-81e23fd13c6c: 2
## 07ccb4e9-a2a9-4bfd-97bd-13873b01977a: 2
## 1426b4bf-f4a5-477c-bbbb-e0e656549764: 2
## 181c6d37-9d8d-4ffa-827b-e3785450ff88: 2
## 1d7ffbe7-6139-412b-8739-8082a63a2b33: 2
## (Other) :528
## patient.biochemical_recurrence
## no :402
## yes : 61
## NA's: 77
##
##
##
##
## patient.bone_scan_results
## abnormal (not related to prostate cancer) : 23
## equivocal : 9
## normal (no evidence of prostate cancer) [cm0]:231
## NA's :277
##
##
##
## patient.clinical_cqcf.country patient.clinical_cqcf.days_to_consent
## united states:441 31 : 14
## germany : 59 62 : 13
## canada : 27 42 : 12
## australia : 8 0 : 10
## moldova : 1 63 : 10
## romania : 1 (Other):451
## (Other) : 3 NA's : 30
## patient.clinical_cqcf.days_to_preop_psa
## 0 : 71
## -33 : 8
## -22 : 7
## 31 : 7
## -18 : 6
## (Other):403
## NA's : 38
## patient.clinical_cqcf.ethnicity
## hispanic or latino : 5
## not hispanic or latino:424
## NA's :111
##
##
##
##
## patient.clinical_cqcf.gleason_score_combined
## 08: 1
## 10: 11
## 6 : 55
## 7 :284
## 8 : 75
## 9 :114
##
## patient.clinical_cqcf.gleason_score_primary
## 05: 1
## 2 : 2
## 3 :235
## 4 :241
## 5 : 61
##
##
## patient.clinical_cqcf.gleason_score_secondary
## 03: 1
## 3 :167
## 4 :285
## 5 : 87
##
##
##
## patient.clinical_cqcf.histological_type
## prostate adenocarcinoma other subtype: 16
## prostate adenocarcinoma acinar type :524
##
##
##
##
##
## patient.clinical_cqcf.history_of_prior_malignancy
## no :509
## yes, history of prior malignancy : 28
## yes, history of synchronous and or bilateral malignancy: 3
##
##
##
##
## patient.clinical_cqcf.normal_tissue_anatomic_site
## other :170
## seminal vesicle: 58
## NA's :312
##
##
##
##
## patient.clinical_cqcf.normal_tissue_proximity
## adjacent (< or = 2cm): 12
## distal (>2cm) :208
## NA's :320
##
##
##
##
## patient.clinical_cqcf.other_anatomic_site_normal_tissue
## blood : 5
## prostate:115
## NA's :420
##
##
##
##
## patient.clinical_cqcf.psa_result_preop
## 4.6 : 14
## 5.2 : 12
## 5.6 : 11
## 5.5 : 10
## 7.4 : 10
## (Other):480
## NA's : 3
## patient.clinical_cqcf.race
## american indian or alaska native: 1
## asian : 12
## black or african american : 64
## white :444
## NA's : 19
##
##
## patient.day_of_form_completion patient.days_to_birth
## 16 : 45 -20805 : 4
## 20 : 31 -23725 : 4
## 5 : 29 -23360 : 3
## 28 : 28 -23458 : 3
## 6 : 28 -15884 : 2
## 23 : 27 (Other):513
## (Other):352 NA's : 11
## patient.days_to_bone_scan_performed patient.days_to_death
## 31 : 11 1329 : 1
## 10 : 10 1855 : 1
## 12 : 10 3467 : 1
## 13 : 10 628 : 1
## 14 : 9 728 : 1
## (Other):208 (Other): 2
## NA's :282 NA's :533
## patient.days_to_diagnostic_computed_tomography_performed
## 11 : 12
## 31 : 12
## 14 : 11
## 10 : 8
## 30 : 8
## (Other):167
## NA's :322
## patient.days_to_diagnostic_mri_performed
## 0 : 3
## 43 : 3
## 45 : 3
## -73 : 2
## -8 : 2
## (Other): 69
## NA's :458
## patient.days_to_first_biochemical_recurrence
## 189 : 3
## 124 : 2
## 131 : 2
## 81 : 2
## 1009 : 1
## (Other): 62
## NA's :468
## patient.days_to_initial_pathologic_diagnosis
## 0 :510
## NA's: 30
##
##
##
##
##
## patient.days_to_last_followup patient.diagnostic_ct_abd_pelvis_performed
## 62 : 6 no :205
## 91 : 6 yes :220
## 31 : 5 NA's:115
## 822 : 5
## 285 : 4
## (Other):507
## NA's : 7
## patient.diagnostic_ct_abd_pelvis_results.diagnostic_ct_abd_pelvis_result
## equivocal : 5
## extraprostatic extension localized (e.g. seminal vesicles) : 5
## extraprostatic extension (regional lymphadenopathy)[e.g. cn1]: 6
## no evidence of extraprostatic extension :202
## NA's :322
##
##
## patient.diagnostic_mri_performed
## no :332
## yes : 85
## NA's:123
##
##
##
##
## patient.diagnostic_mri_results.diagnostic_mri_result
## equivocal : 5
## extraprostatic extension localized (e.g. seminal vesicles): 23
## no evidence of extraprostatic extension : 53
## NA's :459
##
##
##
## patient.diagnostic_mri_results.diagnostic_mri_result-2
## equivocal : 1
## extraprostatic extension (regional lymphadenopathy) [e.g. cn1]: 3
## NA's :536
##
##
##
##
## patient.drugs.drug-2.bcr_drug_barcode
## tcga-ch-5751-d37730: 1
## tcga-ch-5788-d37734: 1
## tcga-g9-7521-d48748: 1
## tcga-g9-a9s0-d60766: 1
## tcga-hi-7171-d29022: 1
## (Other) : 27
## NA's :508
## patient.drugs.drug-2.bcr_drug_uuid
## 03320f22-90b1-4353-ac00-be36880265e5: 1
## 06103a93-83eb-418a-9522-2ff6efb7c941: 1
## 0af1ea65-d032-4370-8744-f0016808415b: 1
## 13e4a7e5-1c0b-4702-95a8-801835da59e4: 1
## 187f4262-f427-4804-994f-8b01714a052a: 1
## (Other) : 27
## NA's :508
## patient.drugs.drug-2.clinical_trail_drug_classification
## n/a : 2
## NA's:538
##
##
##
##
##
## patient.drugs.drug-2.day_of_form_completion
## 13 : 7
## 25 : 5
## 27 : 3
## 2 : 2
## 20 : 2
## (Other): 13
## NA's :508
## patient.drugs.drug-2.days_to_drug_therapy_end
## 1036 : 1
## 1228 : 1
## 126 : 1
## 1461 : 1
## 1527 : 1
## (Other): 12
## NA's :523
## patient.drugs.drug-2.days_to_drug_therapy_start
## 207 : 2
## 1078 : 1
## 115 : 1
## 1163 : 1
## 1219 : 1
## (Other): 25
## NA's :509
## patient.drugs.drug-2.drug_name
## lupron : 9
## casodex : 6
## zoladex : 4
## eligard : 2
## leuprolide: 2
## (Other) : 9
## NA's :508
## patient.drugs.drug-2.measure_of_response
## clinical progressive disease: 2
## complete response : 11
## partial response : 3
## stable disease : 2
## NA's :522
##
##
## patient.drugs.drug-2.month_of_form_completion
## 4 : 9
## 3 : 5
## 12 : 4
## 8 : 4
## 10 : 2
## (Other): 8
## NA's :508
## patient.drugs.drug-2.regimen_indication
## recurrence: 1
## NA's :539
##
##
##
##
##
## patient.drugs.drug-2.therapy_ongoing
## no : 18
## yes : 14
## NA's:508
##
##
##
##
## patient.drugs.drug-2.therapy_types.therapy_type
## hormone therapy: 32
## NA's :508
##
##
##
##
##
## patient.drugs.drug-2.tx_on_clinical_trial
## no : 27
## yes : 4
## NA's:509
##
##
##
##
## patient.drugs.drug-2.year_of_form_completion
## 2012: 3
## 2013: 1
## 2014: 27
## 2015: 1
## NA's:508
##
##
## patient.drugs.drug-3.bcr_drug_barcode
## tcga-ch-5751-d37731: 1
## tcga-g9-7521-d48749: 1
## tcga-g9-a9s0-d60767: 1
## tcga-hi-7171-d29023: 1
## tcga-kk-a6e0-d62512: 1
## (Other) : 7
## NA's :528
## patient.drugs.drug-3.bcr_drug_uuid
## 03feb539-c786-41e6-9134-3c83d062c466: 1
## 057173bd-c7f4-4750-882a-b9b51145c98a: 1
## 1572b2f1-99f4-4b83-b2e3-67c95c87a27e: 1
## 47e9f8b2-f44d-49a1-aced-7b3ce938ad99: 1
## 4a16143e-2d4f-4674-971c-3e045626f7aa: 1
## (Other) : 7
## NA's :528
## patient.drugs.drug-3.clinical_trail_drug_classification
## n/a : 1
## NA's:539
##
##
##
##
##
## patient.drugs.drug-3.day_of_form_completion
## 13 : 1
## 16 : 1
## 18 : 1
## 2 : 1
## 20 : 1
## (Other): 7
## NA's :528
## patient.drugs.drug-3.days_to_drug_therapy_end
## 1339 : 1
## 1630 : 1
## 2170 : 1
## 3467 : 1
## 605 : 1
## (Other): 2
## NA's :533
## patient.drugs.drug-3.days_to_drug_therapy_start
## 1183 : 1
## 1287 : 1
## 1600 : 1
## 1897 : 1
## 2431 : 1
## (Other): 6
## NA's :529
## patient.drugs.drug-3.drug_name
## casodex : 4
## degarelix : 1
## lupron : 5
## taxotere : 1
## zoledronic acid: 1
## NA's :528
##
## patient.drugs.drug-3.measure_of_response
## clinical progressive disease: 3
## complete response : 1
## partial response : 2
## NA's :534
##
##
##
## patient.drugs.drug-3.month_of_form_completion
## 4 : 2
## 7 : 2
## 8 : 2
## 11 : 1
## 12 : 1
## (Other): 4
## NA's :528
## patient.drugs.drug-3.therapy_ongoing
## no : 8
## yes : 4
## NA's:528
##
##
##
##
## patient.drugs.drug-3.therapy_types.therapy_type
## ancillary : 1
## chemotherapy : 1
## hormone therapy: 10
## NA's :528
##
##
##
## patient.drugs.drug-3.tx_on_clinical_trial
## no : 11
## NA's:529
##
##
##
##
##
## patient.drugs.drug-3.year_of_form_completion
## 2012: 2
## 2013: 1
## 2014: 9
## NA's:528
##
##
##
## patient.drugs.drug-4.bcr_drug_barcode
## tcga-g9-a9s0-d60768: 1
## tcga-hi-7171-d29024: 1
## tcga-kk-a8ii-d62413: 1
## tcga-yl-a8sb-d67267: 1
## tcga-yl-a8sp-d59011: 1
## tcga-yl-a9wk-d58528: 1
## NA's :534
## patient.drugs.drug-4.bcr_drug_uuid
## 17d96cc4-b3a0-46c2-af8a-5454ad7e54af: 1
## 3780b9f2-c2ca-4db2-a58e-6f6fa6a66a55: 1
## 4e9d83b0-0e1a-4de9-8edc-6777986d8f98: 1
## 4f7e50a0-c217-4635-a1e3-677d4b516094: 1
## 5c3ec5b6-18d2-46be-9fd9-3703a2fa6fbb: 1
## 770b5c2b-e349-463b-a7d8-ab2d0ee929fc: 1
## NA's :534
## patient.drugs.drug-4.day_of_form_completion
## 13 : 1
## 16 : 1
## 22 : 1
## 25 : 1
## 3 : 1
## 30 : 1
## NA's:534
## patient.drugs.drug-4.days_to_drug_therapy_end
## 2170: 1
## 2738: 1
## 727 : 1
## NA's:537
##
##
##
## patient.drugs.drug-4.days_to_drug_therapy_start
## 1609: 1
## 1814: 1
## 1891: 1
## 2516: 1
## 559 : 1
## 727 : 1
## NA's:534
## patient.drugs.drug-4.drug_name
## cabazitaxel: 1
## casodex : 3
## docetaxel : 1
## lupron : 1
## NA's :534
##
##
## patient.drugs.drug-4.measure_of_response
## clinical progressive disease: 2
## partial response : 1
## NA's :537
##
##
##
##
## patient.drugs.drug-4.month_of_form_completion
## 11 : 1
## 2 : 1
## 4 : 2
## 6 : 1
## 8 : 1
## NA's:534
##
## patient.drugs.drug-4.therapy_ongoing
## no : 4
## yes : 2
## NA's:534
##
##
##
##
## patient.drugs.drug-4.therapy_types.therapy_type
## chemotherapy : 2
## hormone therapy: 4
## NA's :534
##
##
##
##
## patient.drugs.drug-4.tx_on_clinical_trial
## no : 5
## NA's:535
##
##
##
##
##
## patient.drugs.drug-4.year_of_form_completion
## 2012: 1
## 2014: 5
## NA's:534
##
##
##
##
## patient.drugs.drug-5.bcr_drug_barcode
## tcga-kk-a8ii-d62416: 1
## NA's :539
##
##
##
##
##
## patient.drugs.drug.bcr_drug_barcode
## tcga-v1-a9o5-d70126: 2
## tcga-4l-aa1f-d67927: 1
## tcga-ch-5741-d37729: 1
## tcga-ch-5751-d37727: 1
## tcga-ch-5752-d37732: 1
## (Other) : 60
## NA's :474
## patient.drugs.drug.bcr_drug_uuid
## cf129345-f428-483b-bf72-c431f6bba535: 2
## 00ca7115-7773-4773-9ac4-ffccd1ccf33b: 1
## 0f689e8f-3720-4bb6-9b8d-3fd7bf4a4164: 1
## 1383f0a9-3896-485b-8575-e3412a373b34: 1
## 1855423a-82d5-40a1-8789-9cb1346acf7d: 1
## (Other) : 60
## NA's :474
## patient.drugs.drug.clinical_trail_drug_classification
## hormonal treatment: 1
## n/a : 4
## NA's :535
##
##
##
##
## patient.drugs.drug.day_of_form_completion
## 25 : 10
## 13 : 8
## 27 : 7
## 10 : 4
## 20 : 4
## (Other): 33
## NA's :474
## patient.drugs.drug.days_to_drug_therapy_end
## 1106 : 1
## 143 : 1
## 1455 : 1
## 162 : 1
## 1862 : 1
## (Other): 21
## NA's :514
## patient.drugs.drug.days_to_drug_therapy_start
## 151 : 4
## 118 : 3
## 179 : 2
## 207 : 2
## 209 : 2
## (Other): 53
## NA's :474
## patient.drugs.drug.drug_name
## lupron : 16
## casodex : 14
## eligard : 6
## leuprolide: 4
## zoladex : 4
## (Other) : 21
## NA's :475
## patient.drugs.drug.measure_of_response
## clinical progressive disease: 2
## complete response : 19
## partial response : 2
## stable disease : 1
## NA's :516
##
##
## patient.drugs.drug.month_of_form_completion
## 8 : 12
## 4 : 11
## 3 : 9
## 1 : 8
## 12 : 6
## (Other): 20
## NA's :474
## patient.drugs.drug.number_cycles patient.drugs.drug.prescribed_dose
## 13 : 1 22.5: 1
## NA's:539 400 : 1
## NA's:538
##
##
##
##
## patient.drugs.drug.prescribed_dose_units
## mg : 2
## NA's:538
##
##
##
##
##
## patient.drugs.drug.therapy_ongoing
## no : 26
## yes : 39
## NA's:475
##
##
##
##
## patient.drugs.drug.therapy_types.therapy_type
## chemotherapy : 3
## hormone therapy: 63
## NA's :474
##
##
##
##
## patient.drugs.drug.tx_on_clinical_trial
## no : 58
## yes : 6
## NA's:476
##
##
##
##
## patient.drugs.drug.year_of_form_completion patient.ethnicity
## 2012: 7 not hispanic or latino:197
## 2013: 4 NA's :343
## 2014: 48
## 2015: 7
## NA's:474
##
##
## patient.follow_ups.follow_up-2.additional_pharmaceutical_therapy
## no : 4
## yes : 1
## NA's:535
##
##
##
##
## patient.follow_ups.follow_up-2.bcr_followup_barcode
## tcga-ej-7781-f60365: 2
## tcga-ej-7782-f60366: 2
## tcga-ej-7783-f60370: 2
## tcga-ej-7784-f60372: 2
## tcga-ej-7793-f60362: 2
## (Other) : 26
## NA's :504
## patient.follow_ups.follow_up-2.bcr_followup_uuid
## 0a531879-7216-4649-9d57-18ce9d6de7e4: 2
## 2fe6895e-1d5b-453a-b8ca-c51311f587d2: 2
## 45f62940-8821-43ac-bc5b-268a9ba14895: 2
## 601cf690-ca85-4f26-ae09-9ac8daba8d86: 2
## 84754d49-164b-4e0c-bb40-690d1f151cb3: 2
## (Other) : 26
## NA's :504
## patient.follow_ups.follow_up-2.day_of_form_completion
## 6 : 19
## 11 : 4
## 5 : 4
## 30 : 3
## 20 : 2
## (Other): 4
## NA's :504
## patient.follow_ups.follow_up-2.days_to_first_biochemical_recurrence
## 1443: 2
## NA's:538
##
##
##
##
##
## patient.follow_ups.follow_up-2.days_to_last_followup
## 1167 : 2
## 1378 : 2
## 1443 : 2
## 2465 : 2
## 606 : 2
## (Other): 23
## NA's :507
## patient.follow_ups.follow_up-2.days_to_new_tumor_event_after_initial_treatment
## 1285: 1
## 425 : 1
## 974 : 1
## NA's:537
##
##
##
## patient.follow_ups.follow_up-2.followup_case_report_form_submission_reason
## additional new tumor event : 2
## scheduled follow-up submission: 34
## NA's :504
##
##
##
##
## patient.follow_ups.follow_up-2.followup_treatment_success
## complete remission/response: 32
## progressive disease : 4
## NA's :504
##
##
##
##
## patient.follow_ups.follow_up-2.lost_follow_up
## no : 30
## yes : 4
## NA's:506
##
##
##
##
## patient.follow_ups.follow_up-2.month_of_form_completion
## 10 : 2
## 2 : 2
## 3 : 1
## 4 : 3
## 5 : 1
## 6 : 27
## NA's:504
## patient.follow_ups.follow_up-2.new_neoplasm_event_type
## biochemical evidence of disease: 2
## new primary tumor : 3
## NA's :535
##
##
##
##
## patient.follow_ups.follow_up-2.new_tumor_event_after_initial_treatment
## no : 27
## yes : 5
## NA's:508
##
##
##
##
## patient.follow_ups.follow_up-2.person_neoplasm_cancer_status
## tumor free: 29
## with tumor: 3
## NA's :508
##
##
##
##
## patient.follow_ups.follow_up-2.primary_therapy_outcome_success
## complete remission/response: 27
## progressive disease : 2
## NA's :511
##
##
##
##
## patient.follow_ups.follow_up-2.radiation_therapy
## no : 29
## NA's:511
##
##
##
##
##
## patient.follow_ups.follow_up-2.vital_status
## alive: 32
## NA's :508
##
##
##
##
##
## patient.follow_ups.follow_up-2.year_of_form_completion
## 2012: 2
## 2013: 8
## 2014: 26
## NA's:504
##
##
##
## patient.follow_ups.follow_up.additional_pharmaceutical_therapy
## no : 34
## yes : 18
## NA's:488
##
##
##
##
## patient.follow_ups.follow_up.additional_radiation_therapy
## no : 35
## yes : 17
## NA's:488
##
##
##
##
## patient.follow_ups.follow_up.bcr_followup_barcode
## tcga-ch-5767-f28999: 2
## tcga-ch-5768-f28998: 2
## tcga-ej-7115-f64799: 2
## tcga-ej-7123-f64800: 2
## tcga-ej-7125-f64801: 2
## (Other) :409
## NA's :121
## patient.follow_ups.follow_up.bcr_followup_uuid
## 00c8611c-dc2f-4a9c-9157-5fbdd688327e: 2
## 014bfbba-5bb0-4b05-9065-765c982720f7: 2
## 053bb5a0-578f-42d3-87fe-9ab36d9d8826: 2
## 09804433-748d-4bcd-a78c-591903061a38: 2
## 0cc76757-83da-4ae3-8ab6-328b0ce091a8: 2
## (Other) :409
## NA's :121
## patient.follow_ups.follow_up.day_of_form_completion
## 24 : 39
## 3 : 36
## 11 : 35
## 12 : 26
## 10 : 24
## (Other):259
## NA's :121
## patient.follow_ups.follow_up.days_to_death
## 1329: 1
## 1855: 1
## 3467: 1
## 3502: 1
## 728 : 1
## 791 : 1
## NA's:534
## patient.follow_ups.follow_up.days_to_first_biochemical_recurrence
## 124 : 2
## 420 : 2
## 1009 : 1
## 1060 : 1
## 1068 : 1
## (Other): 43
## NA's :490
## patient.follow_ups.follow_up.days_to_last_followup
## 396 : 4
## 1434 : 3
## 425 : 3
## 442 : 3
## 686 : 3
## (Other):395
## NA's :129
## patient.follow_ups.follow_up.days_to_new_tumor_event_after_initial_treatment
## 420 : 2
## 1006 : 1
## 1009 : 1
## 1060 : 1
## 1068 : 1
## (Other): 36
## NA's :498
## patient.follow_ups.follow_up.days_to_second_biochemical_recurrence
## 1523 : 1
## 1687 : 1
## 1756 : 1
## 1934 : 1
## 2019 : 1
## (Other): 4
## NA's :531
## patient.follow_ups.follow_up.days_to_third_biochemical_recurrence
## 2011: 1
## 631 : 1
## 655 : 1
## NA's:537
##
##
##
## patient.follow_ups.follow_up.followup_case_report_form_submission_reason
## additional new tumor event : 18
## scheduled follow-up submission:399
## NA's :123
##
##
##
##
## patient.follow_ups.follow_up.followup_treatment_success
## complete remission/response:312
## partial remission/response : 13
## progressive disease : 15
## stable disease : 35
## NA's :165
##
##
## patient.follow_ups.follow_up.lost_follow_up
## no :360
## yes : 33
## NA's:147
##
##
##
##
## patient.follow_ups.follow_up.month_of_form_completion
## 9 :117
## 2 : 74
## 8 : 60
## 11 : 44
## 1 : 33
## (Other): 91
## NA's :121
## patient.follow_ups.follow_up.new_neoplasm_event_occurrence_anatomic_site
## bone : 4
## lung : 1
## other, specify: 4
## NA's :531
##
##
##
## patient.follow_ups.follow_up.new_neoplasm_event_type
## biochemical evidence of disease: 45
## distant metastasis : 5
## locoregional recurrence : 3
## new primary tumor : 4
## NA's :483
##
##
## patient.follow_ups.follow_up.new_neoplasm_occurrence_anatomic_site_text
## biochemical recurrence only: 2
## lung and liver : 1
## neck : 1
## NA's :536
##
##
##
## patient.follow_ups.follow_up.new_tumor_event_after_initial_treatment
## no :333
## yes : 60
## NA's:147
##
##
##
##
## patient.follow_ups.follow_up.patient_death_reason
## prostate cancer: 2
## NA's :538
##
##
##
##
##
## patient.follow_ups.follow_up.person_neoplasm_cancer_status
## tumor free:300
## with tumor: 41
## NA's :199
##
##
##
##
## patient.follow_ups.follow_up.primary_therapy_outcome_success
## complete remission/response:328
## partial remission/response : 27
## progressive disease : 24
## stable disease : 22
## NA's :139
##
##
## patient.follow_ups.follow_up.radiation_therapy
## no :353
## yes : 49
## NA's:138
##
##
##
##
## patient.follow_ups.follow_up.source_of_patient_death_reason
## medical record: 5
## NA's :535
##
##
##
##
##
## patient.follow_ups.follow_up.targeted_molecular_therapy
## no :353
## yes : 46
## NA's:141
##
##
##
##
## patient.follow_ups.follow_up.tumor_progression_post_ht
## no : 4
## yes : 12
## NA's:524
##
##
##
##
## patient.follow_ups.follow_up.type_ofprogression_of_disease_ht
## biochemical recurrence: 10
## distant metastasis : 3
## NA's :527
##
##
##
##
## patient.follow_ups.follow_up.vital_status
## alive:411
## dead : 6
## NA's :123
##
##
##
##
## patient.follow_ups.follow_up.year_of_form_completion
## 2012: 29
## 2013:116
## 2014:218
## 2015: 56
## NA's:121
##
##
## patient.histological_type
## prostate adenocarcinoma other subtype: 16
## prostate adenocarcinoma acinar type :524
##
##
##
##
##
## patient.history_of_neoadjuvant_treatment patient.icd_10
## no :539 c61 :255
## NA's: 1 c61.9:284
## NA's : 1
##
##
##
##
## patient.icd_o_3_histology
## 8140/3:284
## 8255/3: 3
## 8480/3: 1
## 8500/3: 10
## 8550/3:242
##
##
## patient.initial_pathologic_diagnosis_method patient.laterality
## core needle biopsy :523 bilateral:474
## transurethral resection (turbt): 12 left : 20
## NA's : 5 right : 37
## NA's : 9
##
##
##
## patient.lymphnodes_examined patient.month_of_form_completion
## no : 79 3 :168
## yes :458 4 :134
## NA's: 3 7 : 59
## 8 : 44
## 1 : 35
## 5 : 30
## (Other): 70
## patient.new_tumor_events.new_tumor_event.additional_pharmaceutical_therapy
## no : 23
## yes : 19
## NA's:498
##
##
##
##
## patient.new_tumor_events.new_tumor_event.additional_radiation_therapy
## no : 21
## yes : 23
## NA's:496
##
##
##
##
## patient.new_tumor_events.new_tumor_event.days_to_new_tumor_event_after_initial_treatment
## 124 : 2
## 1006 : 1
## 1009 : 1
## 1022 : 1
## 105 : 1
## (Other): 56
## NA's :478
## patient.new_tumor_events.new_tumor_event.new_neoplasm_event_occurrence_anatomic_site
## bone : 2
## non-regional / distant lymph nodes: 3
## other, specify : 1
## NA's :534
##
##
##
## patient.new_tumor_events.new_tumor_event.new_neoplasm_event_type
## biochemical evidence of disease: 58
## distant metastasis : 4
## locoregional recurrence : 4
## new primary tumor : 3
## NA's :471
##
##
## patient.new_tumor_events.new_tumor_event.new_neoplasm_occurrence_anatomic_site_text
## melanoma in situ of the right midback: 1
## NA's :539
##
##
##
##
##
## patient.new_tumor_events.new_tumor_event.tumor_progression_post_ht
## no : 39
## yes : 8
## NA's:493
##
##
##
##
## patient.new_tumor_events.new_tumor_event.type_of_progression_after_ht
## biochemical recurrence: 6
## distant metastases : 2
## NA's :532
##
##
##
##
## patient.new_tumor_events.new_tumor_event_after_initial_treatment
## no :249
## yes : 70
## NA's:221
##
##
##
##
## patient.number_of_lymphnodes_examined
## 4 : 35
## 2 : 31
## 6 : 28
## 10 : 27
## 5 : 27
## (Other):315
## NA's : 77
## patient.number_of_lymphnodes_positive_by_he
## 0 :368
## 1 : 42
## 2 : 13
## 3 : 11
## 6 : 4
## (Other): 9
## NA's : 93
## patient.patient_death_reason patient.patient_id
## other non-malignant disease: 1 5761 : 2
## prostate cancer : 2 5767 : 2
## NA's :537 5768 : 2
## 5769 : 2
## 6333 : 2
## 6342 : 2
## (Other):528
## patient.person_neoplasm_cancer_status
## tumor free:354
## with tumor: 82
## NA's :104
##
##
##
##
## patient.primary_therapy_outcome_success
## complete remission/response:161
## partial remission/response : 25
## progressive disease : 14
## stable disease : 20
## NA's :320
##
##
## patient.prior_dx
## no :510
## yes : 13
## yes, history of prior malignancy : 16
## yes, history of synchronous and or bilateral malignancy: 1
##
##
##
## patient.race patient.radiation_therapy
## asian : 2 no :241
## black or african american: 11 yes : 40
## white :189 NA's:259
## NA's :338
##
##
##
## patient.radiations.radiation-2.anatomic_treatment_site
## distant recurrence : 1
## primary tumor field: 1
## NA's :538
##
##
##
##
## patient.radiations.radiation-2.bcr_radiation_barcode
## tcga-fc-a5ob-r61440: 1
## tcga-g9-a9s0-r60771: 1
## NA's :538
##
##
##
##
## patient.radiations.radiation-2.measure_of_response
## radiographic progressive disease: 1
## NA's :539
##
##
##
##
##
## patient.radiations.radiation-2.month_of_form_completion
## 6 : 2
## NA's:538
##
##
##
##
##
## patient.radiations.radiation.anatomic_treatment_site
## distant recurrence : 1
## distant site : 1
## local recurrence : 12
## primary tumor field: 42
## regional site : 11
## NA's :473
##
## patient.radiations.radiation.bcr_radiation_barcode
## tcga-hc-7747-r60209: 2
## tcga-v1-a9o5-r70127: 2
## tcga-ej-5524-r46761: 1
## tcga-ej-a65f-r57144: 1
## tcga-fc-a4ji-r48399: 1
## (Other) : 64
## NA's :469
## patient.radiations.radiation.bcr_radiation_uuid
## b13f9180-c4f6-412f-b6d0-a9ba658b3d5f: 2
## c8610195-3eb5-434d-b13d-e6ca6891b2b8: 2
## 086dc138-5deb-45f5-9566-81593b3ae273: 1
## 0b360fc8-c6ac-47ef-a777-bd95c91dd297: 1
## 0c19b3e6-777d-4f3a-9a5f-ad29a5cbc7ba: 1
## (Other) : 64
## NA's :469
## patient.radiations.radiation.day_of_form_completion
## 25 : 14
## 13 : 7
## 14 : 5
## 28 : 5
## 29 : 5
## (Other): 35
## NA's :469
## patient.radiations.radiation.days_to_radiation_therapy_end
## 210 : 2
## 358 : 2
## 417 : 2
## 851 : 2
## 1128 : 1
## (Other): 59
## NA's :472
## patient.radiations.radiation.days_to_radiation_therapy_start
## 162 : 2
## 206 : 2
## 208 : 2
## 322 : 2
## 103 : 1
## (Other): 60
## NA's :471
## patient.radiations.radiation.measure_of_response
## complete response : 38
## partial response : 9
## radiographic progressive disease: 6
## stable disease : 7
## NA's :480
##
##
## patient.radiations.radiation.month_of_form_completion
## 8 : 15
## 3 : 13
## 1 : 9
## 4 : 9
## 7 : 7
## (Other): 18
## NA's :469
## patient.radiations.radiation.numfractions
## 33 : 12
## 35 : 11
## 37 : 7
## 38 : 5
## 34 : 3
## (Other): 13
## NA's :489
## patient.radiations.radiation.radiation_dosage
## 66 : 14
## 70 : 12
## 6660 : 3
## 6840 : 3
## 6480 : 2
## (Other): 20
## NA's :486
## patient.radiations.radiation.radiation_treatment_ongoing
## no : 69
## yes : 2
## NA's:469
##
##
##
##
## patient.radiations.radiation.radiation_type
## external : 66
## external beam: 2
## NA's :472
##
##
##
##
## patient.radiations.radiation.units
## cgy : 16
## gy : 36
## NA's:488
##
##
##
##
## patient.radiations.radiation.year_of_form_completion
## 2012: 2
## 2013: 9
## 2014: 52
## 2015: 8
## NA's:469
##
##
## patient.residual_tumor patient.source_of_patient_death_reason
## r0 :354 death certificate: 1
## r1 :149 medical record : 4
## r2 : 6 NA's :535
## rx : 15
## NA's: 16
##
##
## patient.stage_event.gleason_grading.gleason_score
## 10: 3
## 6 : 50
## 7 :286
## 8 : 65
## 9 :136
##
##
## patient.stage_event.gleason_grading.primary_pattern
## 2: 2
## 3:225
## 4:264
## 5: 49
##
##
##
## patient.stage_event.gleason_grading.secondary_pattern
## 3:171
## 4:262
## 5:107
##
##
##
##
## patient.stage_event.gleason_grading.tertiary_pattern
## 0 : 1
## 2 : 3
## 3 : 82
## 4 : 41
## 5 : 51
## NA's:362
##
## patient.stage_event.psa.days_to_psa patient.stage_event.psa.psa_value
## 172 : 4 0.1 :165
## 204 : 4 0.03 : 42
## 285 : 4 0.01 : 40
## 91 : 4 0 : 18
## 128 : 3 .01 : 11
## (Other):466 (Other):203
## NA's : 55 NA's : 61
## patient.stage_event.tnm_categories.clinical_categories.clinical_m
## m0 :487
## m1a : 1
## m1c : 1
## NA's: 51
##
##
##
## patient.stage_event.tnm_categories.clinical_categories.clinical_t
## t1c :193
## t2a : 59
## t2b : 57
## t2c : 57
## t3a : 37
## (Other): 34
## NA's :103
## patient.stage_event.tnm_categories.pathologic_categories.pathologic_n
## n0 :386
## n1 : 79
## NA's: 75
##
##
##
##
## patient.stage_event.tnm_categories.pathologic_categories.pathologic_t
## t2a : 15
## t2b : 12
## t2c :190
## t3a :172
## t3b :135
## t4 : 13
## NA's: 3
## patient.targeted_molecular_therapy
## no :239
## yes : 42
## NA's:259
##
##
##
##
## patient.tissue_prospective_collection_indicator
## no :268
## yes:272
##
##
##
##
##
## patient.tissue_retrospective_collection_indicator
## no :272
## yes:268
##
##
##
##
##
## patient.tissue_source_site patient.tumor_levels.tumor_level
## ej :120 apex :311
## hc : 74 base : 19
## g9 : 55 middle: 49
## kk : 45 NA's :161
## ch : 36
## v1 : 30
## (Other):180
## patient.tumor_levels.tumor_level-2 patient.tumor_levels.tumor_level-3
## base : 83 base:170
## middle:211 NA's:370
## NA's :246
##
##
##
##
## patient.vital_status patient.year_of_form_completion
## alive:533 2011: 2
## dead : 7 2012:229
## 2013: 62
## 2014:235
## 2015: 12
##
##
## patient.year_of_initial_pathologic_diagnosis
## 2011 :131
## 2012 : 71
## 2010 : 63
## 2013 : 62
## 2009 : 61
## (Other):122
## NA's : 30
## patient.zone_of_origin sample_type
## central zone : 5 Length:540
## overlapping / multiple zones:125 Class :character
## peripheral zone :136 Mode :character
## transition zone : 8
## NA's :266
##
##
## sample_code vial portion
## Length:540 Length:540 Length:540
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
##
## analyte plate center
## Length:540 Length:540 Length:540
## Class :character Class :character Class :character
## Mode :character Mode :character Mode :character
##
##
##
## Look for association between KLK3 expression and clinical PSA
psadat <- data.frame(psa=as.numeric(as.character(eset$patient.stage_event.psa.psa_value)),
klk3=t(exprs(eset["KLK3", ])))
psadat.complete <- psadat[complete.cases(psadat), ]
plot(KLK3 ~ psa, data=psadat.complete, xlab="clinical PSA", ylab="KLK3 tumor expression", log="xy")## Warning in xy.coords(x, y, xlabel, ylabel, log): 29 x values <= 0 omitted
## from logarithmic plotfit <- lowess(x=psadat.complete$psa, y=psadat.complete$KLK3)
lines(fit, col="red", lw=3)
Is there an association between PSA in the urine and KLK3 in the tumor?
cor.test(x=psadat$KLK3, y=psadat$psa, method="spearman")## Warning in cor.test.default(x = psadat$KLK3, y = psadat$psa, method =
## "spearman"): Cannot compute exact p-value with ties##
## Spearman's rank correlation rho
##
## data: psadat$KLK3 and psadat$psa
## S = 21183000, p-value = 0.0005893
## alternative hypothesis: true rho is not equal to 0
## sample estimates:
## rho
## -0.1564584Clinical psa as a function of ethnicity
Need to get the better race variable with complete data from Tiffany:
table(eset$race)##
## asian black or african american
## 2 11
## white
## 189boxplot(psadat$psa ~ eset$race, ylab="PSA")
MicroRNA dataset
Create and save to disk:
library(Biobase)
eset1 <- extract(prad, "miRNASeq_Gene")
saveRDS(eset1, file="prad_mirna_eset.rds")mergeVecs <- function(x1, x2){
##x1 and x2 are vectors to be merged.
##x1 will be over-written by x2, and in case of conflict, x2 takes priority
if(!identical(length(x1), length(x2))) stop("x1 and x2 must have the same length")
if(!identical(class(x1), class(x2))) stop("x1 and x2 must have the same class")
x1[is.na(x1)] = x2[is.na(x1)]
mismatches <- which(x1 != x2)
if(length(mismatches) > 0){
warning(paste("There were mismatches in positions:", paste0(mismatches, collapse=", ")))
x1[mismatches] = x2[mismatches]
}
return(x1)
}
mergeVecs(x1=c(1, 2, 3, NA), x2=c(2, 2, NA, 4))## Warning in mergeVecs(x1 = c(1, 2, 3, NA), x2 = c(2, 2, NA, 4)): There were
## mismatches in positions: 1## [1] 2 2 3 4eset1$race = mergeVecs(as.character(eset1$patient.clinical_cqcf.race), as.character(eset1$patient.race))
eset1 = eset1[, eset1$race %in% c("white", "black or african american")]DESeq2
countData <- exprs(eset1)
colData <- pData(eset1)
dds <- DESeqDataSetFromMatrix(countData = countData,
colData = colData,
design = ~ batch_number + race)## converting counts to integer mode## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factorsdds <- DESeq(dds)## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 848 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testingres <- results(dds, contrast=c("race", "black or african american", "white"))
res## log2 fold change (MAP): race black or african american vs white
## Wald test p-value: race black or african american vs white
## DataFrame with 1046 rows and 6 columns
## baseMean log2FoldChange lfcSE stat
## <numeric> <numeric> <numeric> <numeric>
## hsa-let-7a-1 33381.49 0.05927754 0.06097997 0.9720821
## hsa-let-7a-2 66427.53 0.05557392 0.06096748 0.9115338
## hsa-let-7a-3 33365.92 0.05785808 0.06074905 0.9524112
## hsa-let-7b 38096.28 0.01559059 0.06725232 0.2318224
## hsa-let-7c 29852.06 0.26869636 0.08075931 3.3271254
## ... ... ... ... ...
## hsa-mir-95 5.692126 0.05668354 0.11481130 0.49371047
## hsa-mir-96 110.185592 0.05623315 0.10721906 0.52446972
## hsa-mir-98 137.149551 0.00464962 0.05136742 0.09051691
## hsa-mir-99a 10770.009268 0.20656289 0.06969620 2.96376118
## hsa-mir-99b 66637.948461 -0.08241718 0.06130383 -1.34440517
## pvalue padj
## <numeric> <numeric>
## hsa-let-7a-1 0.3310096820 0.80766362
## hsa-let-7a-2 0.3620141827 0.82645386
## hsa-let-7a-3 0.3408884798 0.81227333
## hsa-let-7b 0.8166759809 0.96976230
## hsa-let-7c 0.0008774687 0.03838693
## ... ... ...
## hsa-mir-95 0.62151067 0.93250979
## hsa-mir-96 0.59995188 0.93250979
## hsa-mir-98 0.92787645 0.98779169
## hsa-mir-99a 0.00303904 0.08080911
## hsa-mir-99b 0.17881740 0.66132487write.csv(res, file="DESeq2_results.csv")res.sig <- res[which(res$padj < 0.05), ]
res.sig <- res.sig[order(res.sig$pvalue), ]
as.matrix(res.sig)## baseMean log2FoldChange lfcSE stat
## hsa-mir-1304 3.376936e+00 1.3193097 0.14133438 9.334669
## hsa-mir-767 2.082448e+00 0.7613924 0.14228032 5.351354
## hsa-mir-105-2 1.494232e+00 0.6720750 0.14077383 4.774148
## hsa-mir-3647 1.513634e+01 0.4711865 0.10838819 4.347213
## hsa-mir-105-1 1.366677e+00 0.6114070 0.14082390 4.341643
## hsa-mir-3117 2.007749e+00 -0.6026826 0.14574813 -4.135096
## hsa-mir-3651 4.681865e+00 0.5657764 0.14544036 3.890092
## hsa-mir-130b 4.505824e+01 0.3492794 0.09069825 3.851005
## hsa-mir-628 2.748908e+01 0.2452595 0.06742508 3.637511
## hsa-mir-1266 1.097473e+01 -0.3756648 0.10888747 -3.450027
## hsa-mir-346 4.051674e-01 0.5068155 0.14975427 3.384315
## hsa-mir-585 9.648963e-01 -0.5062834 0.15085215 -3.356156
## hsa-let-7c 2.985206e+04 0.2686964 0.08075931 3.327125
## hsa-mir-1298 7.507258e+00 -0.5004641 0.15058181 -3.323536
## hsa-mir-202 2.887445e+00 -0.4813606 0.14614070 -3.293816
## hsa-mir-1224 3.135288e+00 0.4870229 0.14809429 3.288600
## pvalue padj
## hsa-mir-1304 1.013070e-20 6.179726e-18
## hsa-mir-767 8.729852e-08 2.662605e-05
## hsa-mir-105-2 1.804701e-06 3.669558e-04
## hsa-mir-3647 1.378786e-05 1.725342e-03
## hsa-mir-105-1 1.414215e-05 1.725342e-03
## hsa-mir-3117 3.548058e-05 3.607192e-03
## hsa-mir-3651 1.002061e-04 8.732242e-03
## hsa-mir-130b 1.176343e-04 8.969615e-03
## hsa-mir-628 2.752854e-04 1.865823e-02
## hsa-mir-1266 5.605297e-04 3.419231e-02
## hsa-mir-346 7.135620e-04 3.838693e-02
## hsa-mir-585 7.903391e-04 3.838693e-02
## hsa-let-7c 8.774687e-04 3.838693e-02
## hsa-mir-1298 8.888388e-04 3.838693e-02
## hsa-mir-202 9.883712e-04 3.838693e-02
## hsa-mir-1224 1.006870e-03 3.838693e-02Not needed, here for posterity. Loading & checking Tiffany's racevar.
Load Tiffany's file with the race variable and make its barcodes equivalent to eset1:
racevar <- read.csv("racevariable.csv", stringsAsFactors = FALSE)
racevar[, 1] <- paste0(racevar[, 1], "-01")
racevar[, 1] <- gsub(".", "-", racevar[, 1], fixed=TRUE)For interests' sake, which patients are in one dataset but not the other?
racevar[, 1][!racevar[, 1] %in% sampleNames(eset1)]## [1] "tcga-2a-a8vt-01" "tcga-2a-a8vv-01" "tcga-2a-a8w1-01"
## [4] "tcga-ch-5751-01" "tcga-ej-5499-01" "tcga-ej-5502-01"
## [7] "tcga-ej-a8fo-01" "tcga-ej-ab20-01" "tcga-fc-7708-01"
## [10] "tcga-fc-a4ji-01" "tcga-g9-6347-01" "tcga-g9-6354-01"
## [13] "tcga-hc-7741-01" "tcga-hc-8212-01" "tcga-j4-8200-01"
## [16] "tcga-j4-aatz-01" "tcga-j9-a8ck-01" "tcga-kc-a4bv-01"
## [19] "tcga-kk-a6e0-01" "tcga-kk-a6e6-01" "tcga-kk-a6e7-01"
## [22] "tcga-kk-a7az-01" "tcga-kk-a8i9-01" "tcga-kk-a8id-01"
## [25] "tcga-m7-a71y-01" "tcga-qu-a6il-01" "tcga-v1-a8ww-01"
## [28] "tcga-v1-a9ol-01" "tcga-v1-a9zk-01" "tcga-vn-a88o-01"
## [31] "tcga-xa-a8jr-01" "tcga-xj-a9dx-01" "tcga-xk-aaja-01"
## [34] "tcga-xq-a8tb-01" "tcga-y6-a8tl-01" "tcga-yj-a8sw-01"
## [37] "tcga-zg-a9l1-01"sampleNames(eset1)[!sampleNames(eset1) %in% racevar[, 1]]## [1] "tcga-ch-5761-11" "tcga-ch-5767-11" "tcga-ch-5768-11"
## [4] "tcga-ch-5769-11" "tcga-ej-7115-11" "tcga-ej-7123-11"
## [7] "tcga-ej-7125-11" "tcga-ej-7314-11" "tcga-ej-7315-11"
## [10] "tcga-ej-7317-11" "tcga-ej-7321-11" "tcga-ej-7327-11"
## [13] "tcga-ej-7328-11" "tcga-ej-7330-11" "tcga-ej-7331-11"
## [16] "tcga-ej-7781-11" "tcga-ej-7782-11" "tcga-ej-7783-11"
## [19] "tcga-ej-7784-11" "tcga-ej-7785-11" "tcga-ej-7786-11"
## [22] "tcga-ej-7789-11" "tcga-ej-7792-11" "tcga-ej-7793-11"
## [25] "tcga-ej-7794-11" "tcga-ej-7797-11" "tcga-g9-6333-11"
## [28] "tcga-g9-6342-11" "tcga-g9-6348-11" "tcga-g9-6351-11"
## [31] "tcga-g9-6356-11" "tcga-g9-6362-11" "tcga-g9-6363-11"
## [34] "tcga-g9-6365-11" "tcga-g9-6384-11" "tcga-g9-6496-11"
## [37] "tcga-g9-6499-11" "tcga-hc-7211-11" "tcga-hc-7737-11"
## [40] "tcga-hc-7738-11" "tcga-hc-7740-11" "tcga-hc-7742-11"
## [43] "tcga-hc-7745-11" "tcga-hc-7747-11" "tcga-hc-7752-11"
## [46] "tcga-hc-7819-11" "tcga-hc-8258-11" "tcga-hc-8259-11"
## [49] "tcga-hc-8260-11" "tcga-hc-8262-11" "tcga-j4-a83j-11"
## [52] "tcga-v1-a9o5-06"Keep only patients in both eset1 and racevar, and match up the rows:
eset2 <- eset1[, sampleNames(eset1) %in% racevar[, 1]]
racevar <- racevar[racevar[, 1] %in% sampleNames(eset2), ]
racevar <- racevar[match(sampleNames(eset2), racevar[, 1]), ]
all.equal(sampleNames(eset2), racevar[, 1])## [1] TRUEAdd racevar[, 2] to eset2:
eset2$racevar <- racevar[, 2]
summary(eset2$racevar == eset2$race)## Mode TRUE NA's
## logical 458 0