rm(list = ls())
#install.packages("cgdsr")
library(cgdsr)
## Please send questions to cbioportal@googlegroups.com
######################################1.1
#CGDS() : Create a CGDS connection object
#Get list of cancer studies at server
mycgds <- CGDS("http://www.cbioportal.org/")
mycgds
## [1] "CGDS: 0x00000000178ff8a8"
# Test the CGDS endpoint URL using a few simple API tests
test(mycgds)
## getCancerStudies... OK
## getCaseLists (1/2) ... OK
## getCaseLists (2/2) ... OK
## getGeneticProfiles (1/2) ... OK
## getGeneticProfiles (2/2) ... OK
## getClinicalData (1/1) ... OK
## getProfileData (1/6) ... OK
## getProfileData (2/6) ... OK
## getProfileData (3/6) ... OK
## getProfileData (4/6) ... OK
## getProfileData (5/6) ... OK
## getProfileData (6/6) ... OK
# Set verbose flag
setVerbose(mycgds, TRUE)
## [1] TRUE
# Connect to a portal instance that requires authetication
mysecurecgds = CGDS("https://cbioportal.mskcc.org/",
token="fd0522cb-7972-40d0-9d83-cb4c14e8a337")
mysecurecgds
## [1] "CGDS: 0x0000000016d21940"
#######################################1.2
#getCancerStudies() : Retrieve a set of available cancer studies
## Get list of cancer studies at server
all_TCGA_studies <- getCancerStudies(mycgds)
## http://www.cbioportal.org/webservice.do?cmd=getCancerStudies&
class(all_TCGA_studies)
## [1] "data.frame"
dim(all_TCGA_studies) #[1] 290 3
## [1] 290 3
head(all_TCGA_studies,3)
## cancer_study_id
## 1 paac_jhu_2014
## 2 mel_tsam_liang_2017
## 3 all_stjude_2015
## name
## 1 Acinar Cell Carcinoma of the Pancreas (JHU, J Pathol 2014)
## 2 Acral Melanoma (TGEN, Genome Res 2017)
## 3 Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015)
## description
## 1 Whole exome sequencing of 23 surgically resected pancreatic carcinomas with acinar differentiation and their matched normals.
## 2 Whole exome sequencing and transcriptome analysis of 34 Acral Melanoma patients (33 with matched normals).
## 3 Comprehensive profiling of infant MLL-rearranged acute lymphoblastic leukemia (MLL-R ALL)
#View(all_TCGA_studies)
######################################1.3 getCaseLists()
#getCaseLists() : Retrieve case lists for a specific cancer study
#For example, within a particular study, only some cases may
#have sequence data, and another subset of cases may have been sequenced and treated with a specific therapeutic protocol.
all_TCGA_studies$cancer_study_id[grep("tcga",all_TCGA_studies$cancer_study_id)]
## [1] "laml_tcga" "laml_tcga_pub"
## [3] "laml_tcga_pan_can_atlas_2018" "acc_tcga"
## [5] "acc_tcga_pan_can_atlas_2018" "sarc_tcga_pub"
## [7] "blca_tcga_pub_2017" "blca_tcga"
## [9] "blca_tcga_pub" "blca_tcga_pan_can_atlas_2018"
## [11] "lgg_tcga" "lgg_tcga_pan_can_atlas_2018"
## [13] "brca_tcga_pub2015" "brca_tcga"
## [15] "brca_tcga_pub" "brca_tcga_pan_can_atlas_2018"
## [17] "cesc_tcga_pan_can_atlas_2018" "cesc_tcga"
## [19] "chol_tcga" "chol_tcga_pan_can_atlas_2018"
## [21] "coadread_tcga" "coadread_tcga_pub"
## [23] "coadread_tcga_pan_can_atlas_2018" "dlbc_tcga_pan_can_atlas_2018"
## [25] "esca_tcga_pan_can_atlas_2018" "esca_tcga"
## [27] "stes_tcga_pub" "gbm_tcga_pub2013"
## [29] "gbm_tcga_pub" "gbm_tcga"
## [31] "gbm_tcga_pan_can_atlas_2018" "hnsc_tcga"
## [33] "hnsc_tcga_pub" "hnsc_tcga_pan_can_atlas_2018"
## [35] "kich_tcga_pub" "kich_tcga"
## [37] "kich_tcga_pan_can_atlas_2018" "kirc_tcga"
## [39] "kirc_tcga_pub" "kirc_tcga_pan_can_atlas_2018"
## [41] "kirp_tcga" "kirp_tcga_pan_can_atlas_2018"
## [43] "lihc_tcga" "lihc_tcga_pan_can_atlas_2018"
## [45] "luad_tcga" "luad_tcga_pub"
## [47] "luad_tcga_pan_can_atlas_2018" "lusc_tcga"
## [49] "lusc_tcga_pub" "lusc_tcga_pan_can_atlas_2018"
## [51] "dlbc_tcga" "lgggbm_tcga_pub"
## [53] "meso_tcga" "meso_tcga_pan_can_atlas_2018"
## [55] "ov_tcga" "ov_tcga_pub"
## [57] "ov_tcga_pan_can_atlas_2018" "nsclc_tcga_broad_2016"
## [59] "paad_tcga" "paad_tcga_pan_can_atlas_2018"
## [61] "thca_tcga_pub" "pcpg_tcga_pub"
## [63] "pcpg_tcga" "pcpg_tcga_pan_can_atlas_2018"
## [65] "prad_tcga_pub" "prad_tcga"
## [67] "prad_tcga_pan_can_atlas_2018" "sarc_tcga"
## [69] "sarc_tcga_pan_can_atlas_2018" "skcm_tcga"
## [71] "skcm_tcga_pan_can_atlas_2018" "stad_tcga"
## [73] "stad_tcga_pub" "stad_tcga_pan_can_atlas_2018"
## [75] "tgct_tcga" "tgct_tcga_pan_can_atlas_2018"
## [77] "thym_tcga" "thym_tcga_pan_can_atlas_2018"
## [79] "thca_tcga" "thca_tcga_pan_can_atlas_2018"
## [81] "ucs_tcga" "ucs_tcga_pan_can_atlas_2018"
## [83] "ucec_tcga" "ucec_tcga_pub"
## [85] "ucec_tcga_pan_can_atlas_2018" "uvm_tcga"
## [87] "uvm_tcga_pan_can_atlas_2018"
c("gbm_tcga") %in% all_TCGA_studies$cancer_study_id #[1] TRUE
## [1] TRUE
#Below we list the current case lists for the TCGA glioblastoma cancer study:
CaseLists <- getCaseLists(mycgds,'gbm_tcga')
## http://www.cbioportal.org/webservice.do?cmd=getCaseLists&cancer_study_id=gbm_tcga
class(CaseLists)
## [1] "data.frame"
head(CaseLists,2)
## case_list_id case_list_name
## 1 gbm_tcga_all All samples
## 2 gbm_tcga_3way_complete Complete samples
## case_list_description cancer_study_id
## 1 All samples (842 samples) 2437
## 2 Samples with mutation, CNA and expression data (136 samples) 2437
## case_ids
## 1 TCGA-02-0001-01 TCGA-02-0003-01 TCGA-02-0006-01 TCGA-02-0007-01 TCGA-02-0009-01 TCGA-02-0010-01 TCGA-02-0011-01 TCGA-02-0014-01 TCGA-02-0021-01 TCGA-02-0024-01 TCGA-02-0027-01 TCGA-02-0028-01 TCGA-02-0033-01 TCGA-02-0034-01 TCGA-02-0037-01 TCGA-02-0038-01 TCGA-02-0043-01 TCGA-02-0046-01 TCGA-02-0047-01 TCGA-02-0052-01 TCGA-02-0054-01 TCGA-02-0055-01 TCGA-02-0057-01 TCGA-02-0058-01 TCGA-02-0060-01 TCGA-06-0875-01 TCGA-06-0876-01 TCGA-06-0877-01 TCGA-06-0878-01 TCGA-06-0879-01 TCGA-06-0881-01 TCGA-06-0882-01 TCGA-12-0670-01 TCGA-12-0818-01 TCGA-12-0819-01 TCGA-12-0820-01 TCGA-12-0821-01 TCGA-12-0822-01 TCGA-12-0826-01 TCGA-12-0827-01 TCGA-12-0828-01 TCGA-12-0829-01 TCGA-14-0787-01 TCGA-14-0789-01 TCGA-14-0813-01 TCGA-14-0817-01 TCGA-14-0867-01 TCGA-14-0871-01 TCGA-16-0846-01 TCGA-16-0848-01 TCGA-16-0849-01 TCGA-16-0850-01 TCGA-16-0861-01 TCGA-06-0650-01 TCGA-06-1804-01 TCGA-06-5408-01 TCGA-06-5410-01 TCGA-06-5411-01 TCGA-06-5412-01 TCGA-06-5413-01 TCGA-06-5856-01 TCGA-06-5858-01 TCGA-06-5859-01 TCGA-06-6389-01 TCGA-06-6390-01 TCGA-06-6391-01 TCGA-14-0781-01 TCGA-15-1444-01 TCGA-19-5947-01 TCGA-19-5950-01 TCGA-19-5951-01 TCGA-19-5952-01 TCGA-19-5954-01 TCGA-19-5955-01 TCGA-19-5956-01 TCGA-19-5958-01 TCGA-19-5959-01 TCGA-19-5960-01 TCGA-26-1442-01 TCGA-28-2501-01 TCGA-28-2510-01 TCGA-28-6450-01 TCGA-32-1979-01 TCGA-32-1980-01 TCGA-41-5651-01 TCGA-76-6191-01 TCGA-76-6192-01 TCGA-76-6193-01 TCGA-76-6282-01 TCGA-76-6285-01 TCGA-81-5910-01 TCGA-87-5896-01 TCGA-06-1806-01 TCGA-06-6388-01 TCGA-06-6693-01 TCGA-06-6694-01 TCGA-06-6695-01 TCGA-06-6697-01 TCGA-06-6698-01 TCGA-06-6699-01 TCGA-06-6700-01 TCGA-06-6701-01 TCGA-14-0740-01 TCGA-14-0862-01 TCGA-14-1043-01 TCGA-14-1395-01 TCGA-14-1450-01 TCGA-19-5953-01 TCGA-26-6173-01 TCGA-26-6174-01 TCGA-28-5211-01 TCGA-41-6646-01 TCGA-74-6573-01 TCGA-74-6575-01 TCGA-74-6577-01 TCGA-74-6578-01 TCGA-74-6581-01 TCGA-74-6584-01 TCGA-76-6280-01 TCGA-76-6283-01 TCGA-76-6286-01 TCGA-76-6656-01 TCGA-76-6657-01 TCGA-76-6660-01 TCGA-76-6661-01 TCGA-76-6662-01 TCGA-76-6663-01 TCGA-76-6664-01 TCGA-81-5911-01 TCGA-06-0155-01 TCGA-06-1084-01 TCGA-06-1086-01 TCGA-06-1087-01 TCGA-12-1088-01 TCGA-12-1089-01 TCGA-12-1090-01 TCGA-12-1091-01 TCGA-12-1092-01 TCGA-12-1093-01 TCGA-12-1094-01 TCGA-12-1095-01 TCGA-12-1096-01 TCGA-12-1097-01 TCGA-12-1098-01 TCGA-12-1099-01 TCGA-14-0736-01 TCGA-14-0783-01 TCGA-14-0786-01 TCGA-14-1034-01 TCGA-14-1396-01 TCGA-14-1401-01 TCGA-14-1402-01 TCGA-14-1451-01 TCGA-14-1452-01 TCGA-14-1453-01 TCGA-14-1454-01 TCGA-14-1459-01 TCGA-15-1446-01 TCGA-15-1447-01 TCGA-15-1449-01 TCGA-16-1045-01 TCGA-16-1047-01 TCGA-16-1055-01 TCGA-16-1056-01 TCGA-16-1060-01 TCGA-16-1062-01 TCGA-16-1063-01 TCGA-19-0955-01 TCGA-19-0960-01 TCGA-19-0962-01 TCGA-19-0963-01 TCGA-19-0964-01 TCGA-19-1392-01 TCGA-26-1438-01 TCGA-26-1440-01 TCGA-26-1443-01 TCGA-19-4065-01 TCGA-02-0064-01 TCGA-02-0069-01 TCGA-02-0071-01 TCGA-02-0074-01 TCGA-02-0075-01 TCGA-02-0080-01 TCGA-02-0083-01 TCGA-02-0085-01 TCGA-02-0086-01 TCGA-02-0089-01 TCGA-02-0099-01 TCGA-02-0102-01 TCGA-02-0107-01 TCGA-02-0113-01 TCGA-02-0114-01 TCGA-02-0115-01 TCGA-02-0116-01 TCGA-06-1800-01 TCGA-06-1801-01 TCGA-06-1802-01 TCGA-06-1805-01 TCGA-12-1598-01 TCGA-12-1599-01 TCGA-12-1600-01 TCGA-12-1602-01 TCGA-14-0812-01 TCGA-14-0865-01 TCGA-14-0866-01 TCGA-14-1037-01 TCGA-14-1455-01 TCGA-14-1458-01 TCGA-14-1794-01 TCGA-14-1795-01 TCGA-14-1821-01 TCGA-14-1823-01 TCGA-14-1825-01 TCGA-14-1827-01 TCGA-14-1829-01 TCGA-16-1460-01 TCGA-19-0957-01 TCGA-19-1385-01 TCGA-19-1386-01 TCGA-19-1387-01 TCGA-19-1388-01 TCGA-19-1389-01 TCGA-19-1786-01 TCGA-19-1788-01 TCGA-19-1789-01 TCGA-19-1791-01 TCGA-26-1799-01 TCGA-27-1830-01 TCGA-27-1832-01 TCGA-27-1833-01 TCGA-27-1834-01 TCGA-28-1746-01 TCGA-28-1749-01 TCGA-28-1750-01 TCGA-28-1751-01 TCGA-28-1752-01 TCGA-28-1755-01 TCGA-28-1757-01 TCGA-28-1760-01 TCGA-02-2466-01 TCGA-02-2470-01 TCGA-02-2483-01 TCGA-02-2485-01 TCGA-02-2486-01 TCGA-06-2557-01 TCGA-06-2558-01 TCGA-06-2559-01 TCGA-06-2561-01 TCGA-06-2562-01 TCGA-06-2563-01 TCGA-06-2564-01 TCGA-06-2565-01 TCGA-06-2566-01 TCGA-06-2567-01 TCGA-06-2569-01 TCGA-06-2570-01 TCGA-14-0790-01 TCGA-14-1456-01 TCGA-14-2554-01 TCGA-27-1831-01 TCGA-27-1835-01 TCGA-27-1836-01 TCGA-27-1837-01 TCGA-27-1838-01 TCGA-27-2518-01 TCGA-27-2519-01 TCGA-27-2521-01 TCGA-27-2523-01 TCGA-27-2524-01 TCGA-27-2526-01 TCGA-27-2527-01 TCGA-27-2528-01 TCGA-28-1747-01 TCGA-28-1753-01 TCGA-28-1756-01 TCGA-28-2499-01 TCGA-28-2502-01 TCGA-28-2506-01 TCGA-28-2509-01 TCGA-28-2513-01 TCGA-28-2514-01 TCGA-32-1970-01 TCGA-32-1976-01 TCGA-32-1982-01 TCGA-32-1986-01 TCGA-06-0119-01 TCGA-06-0121-01 TCGA-06-0122-01 TCGA-06-0124-01 TCGA-06-0125-01 TCGA-06-0126-01 TCGA-06-0128-01 TCGA-06-0129-01 TCGA-06-0130-01 TCGA-06-0133-01 TCGA-06-0137-01 TCGA-06-0139-01 TCGA-06-0140-01 TCGA-06-0141-01 TCGA-06-0142-01 TCGA-06-0143-01 TCGA-06-0145-01 TCGA-06-0147-01 TCGA-06-0148-01 TCGA-06-0169-01 TCGA-06-A5U0-01 TCGA-06-A5U1-01 TCGA-06-A6S0-01 TCGA-06-A6S1-01 TCGA-19-A60I-01 TCGA-19-A6J4-01 TCGA-19-A6J5-01 TCGA-OX-A56R-01 TCGA-RR-A6KA-01 TCGA-RR-A6KB-01 TCGA-RR-A6KC-01 TCGA-12-1597-01 TCGA-12-3644-01 TCGA-12-3646-01 TCGA-12-3648-01 TCGA-12-3649-01 TCGA-12-3650-01 TCGA-12-3651-01 TCGA-12-3652-01 TCGA-12-3653-01 TCGA-14-2555-01 TCGA-14-3477-01 TCGA-19-1390-01 TCGA-19-1787-01 TCGA-19-2619-01 TCGA-19-2620-01 TCGA-19-2621-01 TCGA-19-2623-01 TCGA-19-2624-01 TCGA-19-2625-01 TCGA-19-2629-01 TCGA-32-2615-01 TCGA-32-2616-01 TCGA-32-2632-01 TCGA-32-2634-01 TCGA-32-2638-01 TCGA-41-2571-01 TCGA-41-2573-01 TCGA-41-2575-01 TCGA-41-3392-01 TCGA-06-0132-01 TCGA-06-0138-01 TCGA-06-0150-01 TCGA-06-0151-01 TCGA-06-0154-01 TCGA-06-0156-01 TCGA-06-0157-01 TCGA-06-0158-01 TCGA-06-0159-01 TCGA-06-0160-01 TCGA-06-0165-01 TCGA-06-0166-01 TCGA-06-0168-01 TCGA-06-0171-01 TCGA-06-0173-01 TCGA-06-0174-01 TCGA-06-0176-01 TCGA-06-0178-01 TCGA-06-0184-01 TCGA-06-0185-01 TCGA-06-0187-01 TCGA-06-0188-01 TCGA-06-0189-01 TCGA-06-0190-01 TCGA-06-0195-01 TCGA-06-0197-01 TCGA-06-0201-01 TCGA-06-0206-01 TCGA-06-0208-01 TCGA-06-0209-01 TCGA-06-0210-01 TCGA-06-0211-01 TCGA-06-0213-01 TCGA-06-0214-01 TCGA-06-0219-01 TCGA-06-0221-01 TCGA-06-0237-01 TCGA-06-0240-01 TCGA-06-0241-01 TCGA-06-A7TK-01 TCGA-06-A7TL-01 TCGA-26-A7UX-01 TCGA-4W-AA9R-01 TCGA-4W-AA9S-01 TCGA-4W-AA9T-01 TCGA-02-0087-01 TCGA-02-0106-01 TCGA-02-0111-01 TCGA-02-0258-01 TCGA-02-0260-01 TCGA-02-0266-01 TCGA-02-0269-01 TCGA-02-0271-01 TCGA-02-0281-01 TCGA-02-0285-01 TCGA-02-0289-01 TCGA-02-0290-01 TCGA-02-0317-01 TCGA-02-0321-01 TCGA-02-0324-01 TCGA-02-0325-01 TCGA-02-0326-01 TCGA-02-0330-01 TCGA-02-0332-01 TCGA-02-0333-01 TCGA-02-0337-01 TCGA-02-0338-01 TCGA-02-0339-01 TCGA-02-0422-01 TCGA-02-0430-01 TCGA-02-0432-01 TCGA-02-0440-01 TCGA-02-0446-01 TCGA-02-0451-01 TCGA-02-0456-01 TCGA-06-0146-01 TCGA-06-0149-01 TCGA-06-0162-01 TCGA-06-0164-01 TCGA-06-0175-01 TCGA-06-0177-01 TCGA-06-0179-01 TCGA-06-0182-01 TCGA-06-0194-01 TCGA-06-0394-01 TCGA-06-0397-01 TCGA-06-0402-01 TCGA-06-0409-01 TCGA-06-0410-01 TCGA-06-0412-01 TCGA-06-0413-01 TCGA-06-0414-01 TCGA-08-0509-01 TCGA-08-0510-01 TCGA-08-0512-01 TCGA-08-0514-01 TCGA-08-0516-01 TCGA-08-0517-01 TCGA-08-0518-01 TCGA-08-0520-01 TCGA-08-0521-01 TCGA-08-0524-01 TCGA-08-0525-01 TCGA-08-0529-01 TCGA-08-0531-01 TCGA-02-0004-01 TCGA-02-0015-01 TCGA-02-0016-01 TCGA-02-0023-01 TCGA-02-0025-01 TCGA-02-0026-01 TCGA-02-0039-01 TCGA-02-0048-01 TCGA-02-0051-01 TCGA-02-0059-01 TCGA-02-0068-01 TCGA-02-0070-01 TCGA-02-0104-01 TCGA-08-0244-01 TCGA-08-0245-01 TCGA-08-0246-01 TCGA-08-0344-01 TCGA-08-0346-01 TCGA-08-0347-01 TCGA-08-0348-01 TCGA-08-0350-01 TCGA-08-0351-01 TCGA-08-0353-01 TCGA-08-0354-01 TCGA-08-0355-01 TCGA-08-0356-01 TCGA-08-0357-01 TCGA-08-0359-01 TCGA-08-0360-01 TCGA-08-0375-01 TCGA-08-0380-01 TCGA-08-0385-01 TCGA-08-0389-01 TCGA-08-0390-01 TCGA-08-0392-01 TCGA-06-0939-01 TCGA-14-4157-01 TCGA-16-1048-01 TCGA-19-1790-01 TCGA-19-2631-01 TCGA-19-4068-01 TCGA-26-1439-01 TCGA-32-1973-01 TCGA-32-1977-01 TCGA-32-1978-01 TCGA-32-1987-01 TCGA-32-1991-01 TCGA-32-2491-01 TCGA-32-2494-01 TCGA-32-2495-01 TCGA-32-4208-01 TCGA-32-4210-01 TCGA-32-4211-01 TCGA-32-4213-01 TCGA-32-4719-01 TCGA-41-2572-01 TCGA-41-3393-01 TCGA-41-3915-01 TCGA-41-4097-01 TCGA-02-0079-01 TCGA-02-0084-01 TCGA-06-0127-01 TCGA-06-0152-01 TCGA-06-0238-01 TCGA-06-0644-01 TCGA-06-0645-01 TCGA-06-0646-01 TCGA-06-0648-01 TCGA-08-0345-01 TCGA-08-0349-01 TCGA-08-0352-01 TCGA-08-0358-01 TCGA-08-0373-01 TCGA-08-0386-01 TCGA-12-0615-01 TCGA-12-0616-01 TCGA-12-0618-01 TCGA-12-0619-01 TCGA-12-0620-01 TCGA-06-5414-01 TCGA-06-5415-01 TCGA-06-5416-01 TCGA-06-5417-01 TCGA-06-5418-01 TCGA-12-5295-01 TCGA-12-5299-01 TCGA-12-5301-01 TCGA-26-5132-01 TCGA-26-5133-01 TCGA-26-5134-01 TCGA-26-5135-01 TCGA-26-5136-01 TCGA-26-5139-01 TCGA-28-5204-01 TCGA-28-5207-01 TCGA-28-5208-01 TCGA-28-5209-01 TCGA-28-5213-01 TCGA-28-5214-01 TCGA-28-5215-01 TCGA-28-5216-01 TCGA-28-5218-01 TCGA-28-5219-01 TCGA-28-5220-01 TCGA-32-5222-01 TCGA-76-4925-01 TCGA-76-4926-01 TCGA-76-4927-01 TCGA-76-4928-01 TCGA-76-4929-01 TCGA-76-4931-01 TCGA-76-4932-01 TCGA-76-4934-01 TCGA-76-4935-01 TCGA-06-0192-01 TCGA-06-0216-01 TCGA-06-0649-01 TCGA-06-0686-01 TCGA-06-0743-01 TCGA-06-0744-01 TCGA-06-0745-01 TCGA-06-0747-01 TCGA-06-0749-01 TCGA-06-0750-01 TCGA-12-0654-01 TCGA-12-0656-01 TCGA-12-0657-01 TCGA-12-0662-01 TCGA-12-0688-01 TCGA-12-0691-01 TCGA-12-0692-01 TCGA-12-0703-01 TCGA-12-0707-01 TCGA-12-0769-01 TCGA-12-0772-01 TCGA-12-0773-01 TCGA-12-0775-01 TCGA-12-0776-01 TCGA-12-0778-01 TCGA-12-0780-01 TCGA-15-0742-01 TCGA-06-0125-02 TCGA-06-0152-02 TCGA-06-0171-02 TCGA-06-0190-02 TCGA-06-0210-02 TCGA-06-0221-02 TCGA-14-0736-02 TCGA-14-1034-02 TCGA-19-0957-02 TCGA-19-1389-02 TCGA-19-4065-02 TCGA-06-0211-02 TCGA-14-1402-02
## 2 TCGA-02-0047-01 TCGA-02-0055-01 TCGA-06-0878-01 TCGA-06-0882-01 TCGA-12-0821-01 TCGA-14-0787-01 TCGA-14-0789-01 TCGA-14-0817-01 TCGA-16-0846-01 TCGA-06-1804-01 TCGA-06-5408-01 TCGA-06-5410-01 TCGA-06-5411-01 TCGA-06-5412-01 TCGA-06-5413-01 TCGA-06-5856-01 TCGA-06-5858-01 TCGA-06-5859-01 TCGA-14-0781-01 TCGA-15-1444-01 TCGA-19-5960-01 TCGA-26-1442-01 TCGA-28-2510-01 TCGA-32-1980-01 TCGA-41-5651-01 TCGA-16-1045-01 TCGA-14-1823-01 TCGA-14-1825-01 TCGA-14-1829-01 TCGA-27-1830-01 TCGA-27-1832-01 TCGA-27-1834-01 TCGA-02-2483-01 TCGA-02-2485-01 TCGA-02-2486-01 TCGA-06-2557-01 TCGA-06-2558-01 TCGA-06-2559-01 TCGA-06-2561-01 TCGA-06-2562-01 TCGA-06-2563-01 TCGA-06-2564-01 TCGA-06-2565-01 TCGA-06-2567-01 TCGA-06-2569-01 TCGA-06-2570-01 TCGA-14-0790-01 TCGA-14-2554-01 TCGA-27-1831-01 TCGA-27-1835-01 TCGA-27-1837-01 TCGA-27-2519-01 TCGA-27-2521-01 TCGA-27-2523-01 TCGA-27-2524-01 TCGA-27-2526-01 TCGA-27-2528-01 TCGA-28-1747-01 TCGA-28-1753-01 TCGA-28-2509-01 TCGA-28-2513-01 TCGA-28-2514-01 TCGA-32-1970-01 TCGA-32-1982-01 TCGA-06-0129-01 TCGA-06-0130-01 TCGA-06-0141-01 TCGA-12-3650-01 TCGA-12-3652-01 TCGA-12-3653-01 TCGA-19-1390-01 TCGA-19-2619-01 TCGA-19-2620-01 TCGA-19-2624-01 TCGA-19-2625-01 TCGA-19-2629-01 TCGA-32-2615-01 TCGA-32-2632-01 TCGA-32-2634-01 TCGA-32-2638-01 TCGA-41-2571-01 TCGA-06-0132-01 TCGA-06-0157-01 TCGA-06-0158-01 TCGA-06-0168-01 TCGA-06-0174-01 TCGA-06-0178-01 TCGA-06-0184-01 TCGA-06-0219-01 TCGA-32-4213-01 TCGA-41-2572-01 TCGA-41-3915-01 TCGA-41-4097-01 TCGA-06-0238-01 TCGA-06-0644-01 TCGA-06-0645-01 TCGA-06-0646-01 TCGA-08-0386-01 TCGA-12-0616-01 TCGA-12-0618-01 TCGA-12-0619-01 TCGA-06-5414-01 TCGA-06-5415-01 TCGA-06-5418-01 TCGA-12-5295-01 TCGA-12-5299-01 TCGA-26-5132-01 TCGA-26-5133-01 TCGA-26-5134-01 TCGA-26-5135-01 TCGA-26-5136-01 TCGA-26-5139-01 TCGA-28-5204-01 TCGA-28-5207-01 TCGA-28-5208-01 TCGA-28-5209-01 TCGA-28-5213-01 TCGA-28-5215-01 TCGA-28-5216-01 TCGA-28-5218-01 TCGA-28-5220-01 TCGA-32-5222-01 TCGA-76-4925-01 TCGA-76-4926-01 TCGA-76-4928-01 TCGA-76-4929-01 TCGA-76-4931-01 TCGA-06-0649-01 TCGA-06-0686-01 TCGA-06-0743-01 TCGA-06-0744-01 TCGA-06-0745-01 TCGA-06-0747-01 TCGA-06-0749-01 TCGA-06-0750-01 TCGA-15-0742-01
dim(CaseLists) #[1] 12 5
## [1] 12 5
######################################1.4 getProfileData()
#getProfileData() : Retrieve genomic profile data for genes and genetic profiles
#This function queries the CGDS API and returns the available genetic profiles,
#e.g. mutation or copy number profiles, stored about a specific cancer study.
#Below we list the current genetic profiles for the TCGA glioblastoma cancer
#study:
c("gbm_tcga") %in% all_TCGA_studies$cancer_study_id #[1] TRUE
## [1] TRUE
GeneticProfiles <- getGeneticProfiles(mycgds,'gbm_tcga')
## http://www.cbioportal.org/webservice.do?cmd=getGeneticProfiles&cancer_study_id=gbm_tcga
class(GeneticProfiles)
## [1] "data.frame"
dim(GeneticProfiles) #[1] 16 6
## [1] 16 6
head(GeneticProfiles,2)
## genetic_profile_id genetic_profile_name
## 1 gbm_tcga_rppa Protein expression (RPPA)
## 2 gbm_tcga_rppa_Zscores Protein expression Z-scores (RPPA)
## genetic_profile_description
## 1 Protein expression measured by reverse-phase protein array
## 2 Protein expression, measured by reverse-phase protein array, Z-scores
## cancer_study_id genetic_alteration_type show_profile_in_analysis_tab
## 1 2437 PROTEIN_LEVEL false
## 2 2437 PROTEIN_LEVEL true
####################################1.5 getProfileData()
#2.5 getProfileData() : Retrieve genomic profile data for
#genes and genetic profiles
#Below we are retrieving mRNA
#expression and copy number alteration genetic profiles for the NF1 gene in all
#samples of the TCGA glioblastoma cancer study
"gbm_tcga_gistic" %in% GeneticProfiles$genetic_profile_id #[1] TRUE
## [1] TRUE
"gbm_tcga_mrna" %in% GeneticProfiles$genetic_profile_id #[1] TRUE
## [1] TRUE
"gbm_tcga_all" %in% CaseLists$case_list_id #[1] TRUE
## [1] TRUE
?getProfileData
## starting httpd help server ...
## done
NF1 <- getProfileData(mycgds, "NF1", c("gbm_tcga_gistic","gbm_tcga_mrna"), caseList = "gbm_tcga_all")
## http://www.cbioportal.org/webservice.do?cmd=getProfileData&gene_list=NF1&genetic_profile_id=gbm_tcga_gistic,gbm_tcga_mrna&id_type=gene_symbol&case_set_id=gbm_tcga_all
class(NF1)
## [1] "data.frame"
dim(NF1) #[1] 604 2
## [1] 604 2
head(NF1,6)
## gbm_tcga_gistic gbm_tcga_mrna
## TCGA.02.0001.01 -1 NaN
## TCGA.02.0003.01 0 NaN
## TCGA.02.0006.01 0 NaN
## TCGA.02.0007.01 0 NaN
## TCGA.02.0009.01 0 NaN
## TCGA.02.0010.01 0 NaN
#In the next example, we are retrieving mRNA
#expression data for the MDM2 and MDM4 genes:
MDM2_4 <- getProfileData(mycgds, c("MDM2","MDM4"), c("gbm_tcga_gistic"), "gbm_tcga_all")
## http://www.cbioportal.org/webservice.do?cmd=getProfileData&gene_list=MDM2,MDM4&genetic_profile_id=gbm_tcga_gistic&id_type=gene_symbol&case_set_id=gbm_tcga_all
dim(MDM2_4)
## [1] 604 2
#####################################1.6 getClinicalData()
# getClinicalData() : Retrieve clinical data for a list of cases
"gbm_tcga_all" %in% CaseLists$case_list_id
## [1] TRUE
ClinicalData <- getClinicalData(mycgds, "gbm_tcga_all")
## http://www.cbioportal.org/webservice.do?cmd=getClinicalData&case_set_id=gbm_tcga_all
class(ClinicalData)
## [1] "data.frame"
dim(ClinicalData) #[1] 604 2
## [1] 604 52
head(ClinicalData,2)
## AGE CANCER_TYPE CANCER_TYPE_DETAILED DAYS_TO_COLLECTION
## TCGA.32.4213.01 47 Glioma Glioblastoma Multiforme NA
## TCGA.14.1452.01 60 Glioma Glioblastoma Multiforme NA
## DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS DFS_MONTHS
## TCGA.32.4213.01 0 18.43
## TCGA.14.1452.01 0 5.65
## DFS_STATUS ECOG_SCORE ETHNICITY
## TCGA.32.4213.01 1:Recurred/Progressed NA NOT HISPANIC OR LATINO
## TCGA.14.1452.01 1:Recurred/Progressed NA
## FORM_COMPLETION_DATE FRACTION_GENOME_ALTERED
## TCGA.32.4213.01 12/14/10 0.1206
## TCGA.14.1452.01 6/4/09 0.1767
## HISTOLOGICAL_DIAGNOSIS HISTORY_LGG_DX_OF_BRAIN_TISSUE
## TCGA.32.4213.01 Untreated primary (de novo) GBM NO
## TCGA.14.1452.01 Untreated primary (de novo) GBM NO
## HISTORY_NEOADJUVANT_TRTYN HISTORY_OTHER_MALIGNANCY ICD_10
## TCGA.32.4213.01 No C71.9
## TCGA.14.1452.01 No C71.9
## ICD_O_3_HISTOLOGY ICD_O_3_SITE INFORMED_CONSENT_VERIFIED
## TCGA.32.4213.01 9440/3 C71.9 YES
## TCGA.14.1452.01 9440/3 C71.9 YES
## INITIAL_PATHOLOGIC_DX_YEAR IS_FFPE KARNOFSKY_PERFORMANCE_SCORE
## TCGA.32.4213.01 2009 NO NA
## TCGA.14.1452.01 2005 NO 80
## LONGEST_DIMENSION METHOD_OF_INITIAL_SAMPLE_PROCUREMENT
## TCGA.32.4213.01 0.9 Tumor resection
## TCGA.14.1452.01 1.0 Tumor resection
## MUTATION_COUNT NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT
## TCGA.32.4213.01 66
## TCGA.14.1452.01 NA
## OCT_EMBEDDED ONCOTREE_CODE OS_MONTHS OS_STATUS
## TCGA.32.4213.01 NA GBM 19.84 0:LIVING
## TCGA.14.1452.01 NA GBM 7.10 1:DECEASED
## OTHER_PATIENT_ID
## TCGA.32.4213.01 22e0c3ea-9f6d-4d73-9282-17ee4553f436
## TCGA.14.1452.01 f82bfa67-4e72-4a09-8022-a2fe0050090f
## OTHER_SAMPLE_ID
## TCGA.32.4213.01 7d959fc1-ec55-4299-b54e-7777df70ff26
## TCGA.14.1452.01 830aa3d0-7140-4d75-9686-bb17d95b263d
## PATHOLOGY_REPORT_FILE_NAME
## TCGA.32.4213.01 TCGA-32-4213.918246a7-4ae5-463d-b889-011e0ee45efb.pdf
## TCGA.14.1452.01 TCGA-14-1452.f38cb64b-9649-4cc3-a14f-3eabf2c1b299.pdf
## PATHOLOGY_REPORT_UUID PERFORMANCE_STATUS_TIMING
## TCGA.32.4213.01 918246a7-4ae5-463d-b889-011e0ee45efb
## TCGA.14.1452.01 f38cb64b-9649-4cc3-a14f-3eabf2c1b299 Post-Adjuvant Therapy
## PHARMACEUTICAL_TX_ADJUVANT PROSPECTIVE_COLLECTION RACE
## TCGA.32.4213.01 WHITE
## TCGA.14.1452.01 WHITE
## RADIATION_TREATMENT_ADJUVANT RETROSPECTIVE_COLLECTION
## TCGA.32.4213.01
## TCGA.14.1452.01
## SAMPLE_COUNT SAMPLE_INITIAL_WEIGHT SAMPLE_TYPE SAMPLE_TYPE_ID
## TCGA.32.4213.01 1 NA Primary 1
## TCGA.14.1452.01 1 NA Primary 1
## SEX SHORTEST_DIMENSION SITE_OF_TUMOR_TISSUE
## TCGA.32.4213.01 Female 0.2 Brain
## TCGA.14.1452.01 Male 0.2 Brain
## SPECIMEN_SECOND_LONGEST_DIMENSION TISSUE_SOURCE_SITE
## TCGA.32.4213.01 0.7 32
## TCGA.14.1452.01 0.8 14
## TREATMENT_OUTCOME_FIRST_COURSE TUMOR_STATUS VIAL_NUMBER
## TCGA.32.4213.01 WITH TUMOR A
## TCGA.14.1452.01 WITH TUMOR A
####################################2.1
#Example 1: Association of NF1 copy number alteration and mRNA expression in glioblastoma
df = getProfileData(mycgds, "NF1", c("gbm_tcga_gistic","gbm_tcga_mrna"), "gbm_tcga_all")
## http://www.cbioportal.org/webservice.do?cmd=getProfileData&gene_list=NF1&genetic_profile_id=gbm_tcga_gistic,gbm_tcga_mrna&id_type=gene_symbol&case_set_id=gbm_tcga_all
head(df)
## gbm_tcga_gistic gbm_tcga_mrna
## TCGA.02.0001.01 -1 NaN
## TCGA.02.0003.01 0 NaN
## TCGA.02.0006.01 0 NaN
## TCGA.02.0007.01 0 NaN
## TCGA.02.0009.01 0 NaN
## TCGA.02.0010.01 0 NaN
boxplot(df[,2] ~ df[,1], main="NF1 : CNA status vs mRNA expression", xlab="CNA status", ylab = "mRNA expression")
stripchart(df[,2] ~ df[,1], vertical=T, add=T, method="jitter",pch=1,col='red')
##################################2.2
#Example 2: MDM2 and MDM4 mRNA expression levels in glioblastoma
df = getProfileData(mycgds, c("MDM2","MDM4"), "gbm_tcga_mrna", "gbm_tcga_all")
## http://www.cbioportal.org/webservice.do?cmd=getProfileData&gene_list=MDM2,MDM4&genetic_profile_id=gbm_tcga_mrna&id_type=gene_symbol&case_set_id=gbm_tcga_all
head(df)
## MDM2 MDM4
## TCGA.02.0001.01 NaN NaN
## TCGA.02.0003.01 NaN NaN
## TCGA.02.0006.01 NaN NaN
## TCGA.02.0007.01 NaN NaN
## TCGA.02.0009.01 NaN NaN
## TCGA.02.0010.01 NaN NaN
plot(df, main="MDM2 and MDM4 mRNA expression", xlab="MDM2 mRNA expression", ylab="MDM4 mRNA expression")
##################################2.3
#Example 3: Comparing expression of PTEN in primary and metastatic prostate cancer tumors
df.pri = getProfileData(mycgds, "PTEN", "prad_mskcc_mrna_median_Zscores", "prad_mskcc_primary")
## http://www.cbioportal.org/webservice.do?cmd=getProfileData&gene_list=PTEN&genetic_profile_id=prad_mskcc_mrna_median_Zscores&id_type=gene_symbol&case_set_id=prad_mskcc_primary
head(df.pri)
## PTEN
## PCA0001 9.467183
## PCA0002 9.041528
## PCA0003 8.511305
## PCA0004 NaN
## PCA0005 9.413217
## PCA0006 NaN
df.met = getProfileData(mycgds, "PTEN", "prad_mskcc_mrna_median_Zscores","prad_mskcc_mets")
## http://www.cbioportal.org/webservice.do?cmd=getProfileData&gene_list=PTEN&genetic_profile_id=prad_mskcc_mrna_median_Zscores&id_type=gene_symbol&case_set_id=prad_mskcc_mets
head(df.met)
## PTEN
## PCA0182 7.486938
## PCA0183 NaN
## PCA0184 7.578755
## PCA0185 NaN
## PCA0186 NaN
## PCA0187 8.756132
boxplot(list(t(df.pri),t(df.met)), main="PTEN expression in primary and metastatic tumors", xlab="Tumor type", ylab="PTEN mRNA expression",names=c('primary','metastatic'), outpch = NA)
stripchart(list(t(df.pri),t(df.met)), vertical=T, add=T, method="jitter",pch=1,col='red')
