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Last data update: 2014.03.03

R: Information about datasets from TCGA project

checkTCGA

R Documentation

Information about datasets from TCGA project

Description

The checkTCGA function let's to check

DataSets: TCGA datasets' names for current release date and cohort.
Dates: TCGA datasets' dates of release.

Usage

checkTCGA(what, cancerType, date = NULL)

Arguments

`what`	One of `DataSets` or `Dates`.
`cancerType`	A character of length 1 containing abbreviation (Cohort code - http://gdac.broadinstitute.org/) of types of cancers to check for.
`date`	A `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'`.

Details

If what='DataSets' enables to check TCGA datasets' names for current release date and cohort.
If what='Dates' enables to check dates of TCGA datasets' releases.

Value

If what='DataSets' a data.frame of available datasets' names (to pass to the downloadTCGA function) and sizes.
If what='Dates' a vector of available dates to pass to the downloadTCGA function.

Issues

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.

Author(s)

Marcin Kosinski, m.p.kosinski@gmail.com

Examples


############################# 

# names for current release date and cohort
checkTCGA('DataSets', 'BRCA' )
## Not run: 
checkTCGA('DataSets', 'OV', tail(checkTCGA('Dates'))[3] )
#checkTCGA('DataSets', 'OV', checkTCGA('Dates')[5] ) # error

## End(Not run)
# dates of TCGA datasets' releases.
checkTCGA('Dates')

############################# 
## 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()
       })
       

## End(Not run)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RTCGA)
Welcome to the RTCGA (version: 1.2.2).
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCGA/checkTCGA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: checkTCGA
> ### Title: Information about datasets from TCGA project
> ### Aliases: checkTCGA
> 
> ### ** Examples
> 
> 
> ############################# 
> 
> # 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: 
> ##D checkTCGA('DataSets', 'OV', tail(checkTCGA('Dates'))[3] )
> ##D #checkTCGA('DataSets', 'OV', checkTCGA('Dates')[5] ) # error
> ## End(Not run)
> # 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: 
> ##D # TCGA datasets' names availability for 
> ##D # current release date and cancer type.
> ##D 
> ##D releaseDate <- '2015-08-21'
> ##D cancerTypes <- c('OV', 'BRCA')
> ##D 
> ##D cancerTypes %>% sapply(function(element){
> ##D   grep(x = checkTCGA('DataSets', element, releaseDate)[, 1], 
> ##D       pattern = 'humanmethylation450', value = TRUE) %>%
> ##D        as.vector()
> ##D        })
> ##D        
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>