The checkTCGA function let's to check
DataSets: TCGA datasets' names for current release date and cohort.
Dates: TCGA datasets' dates of release.
checkTCGA(what, cancerType, date = NULL)
DataSets or Dates.NULL or character specifying from which date informations should be checked.
By default (date = NULL) the newest available date is used. All available dates can be checked on
http://gdac.broadinstitute.org/runs/ or by using checkTCGA('Dates')
function. Required format 'YYYY-MM-DD'.what='DataSets' a data.frame of available datasets' names (to pass to the downloadTCGA function) and sizes.
what='Dates' a vector of available dates to pass to the downloadTCGA function.
what='DataSets' enables to check TCGA datasets' names for current release date and cohort.
what='Dates' enables to check dates of TCGA datasets' releases.
If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.
RTCGA website http://rtcga.github.io/RTCGA/.
Other RTCGA: RTCGA-package,
boxplotTCGA, convertTCGA,
createTCGA, datasetsTCGA,
downloadTCGA,
expressionsTCGA, heatmapTCGA,
infoTCGA, installTCGA,
kmTCGA, mutationsTCGA,
pcaTCGA, readTCGA,
survivalTCGA, theme_RTCGA
############################# # names for current release date and cohort checkTCGA('DataSets', 'BRCA')#> Size #> 1 37M #> 2 50K #> 3 723K #> 4 135K #> 5 135K #> 6 77K #> 7 78K #> 8 1.5M #> 9 57K #> 10 1.2K #> 11 160K #> 12 3.4M #> 13 86K #> 14 83M #> 15 3.2G #> 16 1.1M #> 17 15M #> 18 2.9M #> 19 44M #> 20 1.3M #> 21 2.6G #> 22 277M #> 23 195M #> 24 298M #> 25 93M #> 26 869M #> 27 249M #> 28 2.8G #> 29 243M #> 30 18M #> 31 18M #> 32 5.3M #> 33 4.6M #> 34 37M #> 35 399M #> 36 10M #> 37 1.1G #> 38 81M #> 39 1.9M #> 40 37M #> 41 1.5G #> 42 6.6M #> 43 7.4M #> Name #> 1 BRCA-FFPE.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz #> 2 BRCA-FFPE.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2016012800.0.0.tar.gz #> 3 BRCA-FFPE.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data.Level_3.2016012800.0.0.tar.gz #> 4 BRCA-FFPE.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg.Level_3.2016012800.0.0.tar.gz #> 5 BRCA-FFPE.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg.Level_3.2016012800.0.0.tar.gz #> 6 BRCA-FFPE.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.Level_3.2016012800.0.0.tar.gz #> 7 BRCA-FFPE.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.Level_3.2016012800.0.0.tar.gz #> 8 BRCA-FFPE.Methylation_Preprocess.Level_3.2016012800.0.0.tar.gz #> 9 BRCA-FFPE.miRseq_Mature_Preprocess.Level_3.2016012800.0.0.tar.gz #> 10 BRCA-FFPE.miRseq_Preprocess.Level_3.2016012800.0.0.tar.gz #> 11 BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz #> 12 BRCA.Merge_Clinical.Level_1.2016012800.0.0.tar.gz #> 13 BRCA.Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.Level_3.2016012800.0.0.tar.gz #> 14 BRCA.Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz #> 15 BRCA.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz #> 16 BRCA.Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2016012800.0.0.tar.gz #> 17 BRCA.Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data.Level_3.2016012800.0.0.tar.gz #> 18 BRCA.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2016012800.0.0.tar.gz #> 19 BRCA.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data.Level_3.2016012800.0.0.tar.gz #> 20 BRCA.Merge_protein_exp__mda_rppa_core__mdanderson_org__Level_3__protein_normalization__data.Level_3.2016012800.0.0.tar.gz #> 21 BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__exon_expression__data.Level_3.2016012800.0.0.tar.gz #> 22 BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz #> 23 BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__splice_junction_expression__data.Level_3.2016012800.0.0.tar.gz #> 24 BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz #> 25 BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0.tar.gz #> 26 BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms__data.Level_3.2016012800.0.0.tar.gz #> 27 BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_isoforms_normalized__data.Level_3.2016012800.0.0.tar.gz #> 28 BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data.Level_3.2016012800.0.0.tar.gz #> 29 BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.Level_3.2016012800.0.0.tar.gz #> 30 BRCA.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg.Level_3.2016012800.0.0.tar.gz #> 31 BRCA.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg.Level_3.2016012800.0.0.tar.gz #> 32 BRCA.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.Level_3.2016012800.0.0.tar.gz #> 33 BRCA.Merge_snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.Level_3.2016012800.0.0.tar.gz #> 34 BRCA.Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3.2016012800.0.0.tar.gz #> 35 BRCA.Methylation_Preprocess.Level_3.2016012800.0.0.tar.gz #> 36 BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz #> 37 BRCA.Mutation_Packager_Coverage.Level_3.2016012800.0.0.tar.gz #> 38 BRCA.Mutation_Packager_Oncotated_Calls.Level_3.2016012800.0.0.tar.gz #> 39 BRCA.RPPA_AnnotateWithGene.Level_3.2016012800.0.0.tar.gz #> 40 BRCA.mRNA_Preprocess_Median.Level_3.2016012800.0.0.tar.gz #> 41 BRCA.mRNAseq_Preprocess.Level_3.2016012800.0.0.tar.gz #> 42 BRCA.miRseq_Mature_Preprocess.Level_3.2016012800.0.0.tar.gz #> 43 BRCA.miRseq_Preprocess.Level_3.2016012800.0.0.tar.gz## Not run: ------------------------------------ # checkTCGA('DataSets', 'OV', tail(checkTCGA('Dates'))[3]) # #checkTCGA('DataSets', 'OV', checkTCGA('Dates')[5]) # error ## --------------------------------------------- # dates of TCGA datasets' releases. checkTCGA('Dates')#> [1] "2011-10-26" "2011-11-15" "2011-11-28" "2011-12-06" "2011-12-30" #> [6] "2012-01-10" "2012-01-24" "2012-02-17" "2012-03-06" "2012-03-21" #> [11] "2012-04-12" "2012-04-25" "2012-05-15" "2012-05-25" "2012-06-06" #> [16] "2012-06-23" "2012-07-07" "2012-07-25" "2012-08-04" "2012-08-25" #> [21] "2012-09-13" "2012-10-04" "2012-10-18" "2012-10-20" "2012-10-24" #> [26] "2012-11-02" "2012-11-14" "2012-12-06" "2012-12-21" "2013-01-16" #> [31] "2013-02-03" "2013-02-22" "2013-03-09" "2013-03-26" "2013-04-06" #> [36] "2013-04-21" "2013-05-08" "2013-05-23" "2013-06-06" "2013-06-23" #> [41] "2013-07-15" "2013-08-09" "2013-09-23" "2013-10-10" "2013-11-14" #> [46] "2013-12-10" "2014-01-15" "2014-02-15" "2014-03-16" "2014-04-16" #> [51] "2014-05-18" "2014-06-14" "2014-07-15" "2014-09-02" "2014-10-17" #> [56] "2014-12-06" "2015-02-02" "2015-02-04" "2015-04-02" "2015-06-01" #> [61] "2015-08-21" "2015-11-01" "2016-01-28"############################# ## Not run: ------------------------------------ # # TCGA datasets' names availability for # # current release date and cancer type. # # releaseDate <- '2015-08-21' # cancerTypes <- c('OV', 'BRCA') # # cancerTypes %>% sapply(function(element){ # grep(x = checkTCGA('DataSets', element, releaseDate)[, 1], # pattern = 'humanmethylation450', value = TRUE) %>% # as.vector() # }) # ## 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