Thank you for asking. It is a matrix. The following is a sample from cgdsr package and
how it can be useful. The users then choose the desired studies from the list. It uses
the printing approach. I can’t store out put of my function as a variable (assgn()) as
specified by my reviewer. when R truncates the output, it is incomplete. User has to
run the code once more and try to manually assign it to a new variable by arrow sign.
Some users even don’t get it after running the code twice.
Regards,
Arman
library(cgdsr)
mycgds = CGDS("http://www.cbioportal.org/")
getCancerStudies(mycgds)[,c(1,2)]
cancer_study_id
1 paac_jhu_2014
2 laml_tcga_pub
3 laml_tcga
4 acyc_fmi_2014
5 acyc_mda_2015
6 acyc_mskcc_2013
7 acyc_sanger_2013
8 acbc_mskcc_2015
9 acc_tcga
10 ampca_bcm_2016
11 blca_mskcc_solit_2014
12 blca_mskcc_solit_2012
13 blca_plasmacytoid_mskcc_2016
14 blca_bgi
15 blca_dfarber_mskcc_2014
16 blca_tcga_pub
17 blca_tcga
18 lgg_tcga
19 brca_metabric
20 brca_bccrc
21 brca_broad
22 brca_sanger
23 brca_tcga_pub2015
24 brca_tcga_pub
25 brca_tcga
26 brca_bccrc_xenograft_2014
27 cellline_ccle_broad
28 cesc_tcga
29 chol_nccs_2013
30 chol_nus_2012
31 chol_tcga
32 lcll_broad_2013
33 cll_iuopa_2015
34 ccrcc_utokyo_2013
35 coadread_dfci_2016
36 coadread_genentech
37 coadread_tcga_pub
38 coadread_tcga
39 coadread_mskcc
40 ctcl_columbia_2015
41 cscc_dfarber_2015
42 pact_jhu_2011
43 desm_broad_2015
44 dlbc_broad_2012
45 esca_broad
46 esca_tcga
47 escc_icgc
48 escc_ucla_2014
49 es_iocurie_2014
50 gbc_shanghai_2014
51 egc_tmucih_2015
52 nsclc_unito_2016
53 skcm_ucla_2016
54 prad_cpcg_2017
55 gct_msk_2016
56 gbm_tcga_pub2013
57 gbm_tcga_pub
58 gbm_tcga
59 hnsc_broad
60 hnsc_jhu
61 hnsc_tcga_pub
62 hnsc_tcga
63 liad_inserm_fr_2014
64 hcc_inserm_fr_2015
65 all_stjude_2013
66 all_stjude_2015
67 panet_shanghai_2013
68 mel_tsam_liang_2017
69 chol_jhu_2013
70 kich_tcga_pub
71 kich_tcga
72 kirc_bgi
73 kirc_tcga_pub
74 kirc_tcga
75 kirp_tcga
76 lihc_amc_prv
77 lihc_riken
78 lihc_tcga
79 lgg_ucsf_2014
80 luad_broad
81 luad_mskcc_2015
82 luad_tcga_pub
83 luad_tcga
84 luad_tsp
85 lusc_tcga_pub
86 lusc_tcga
87 dlbc_tcga
88 prad_mskcc_2017
89 msk_impact_2017
90 mpnst_mskcc
91 plmeso_nyu_2015
92 mcl_idibips_2013
93 mbl_broad_2012
94 mbl_icgc
95 mbl_pcgp
96 mbl_sickkids_2016
97 skcm_broad_dfarber
98 lgggbm_tcga_pub
99 meso_tcga
100 prad_su2c_2015
101 mm_broad
102 ccrcc_irc_2014
103 brca_igr_2015
104 mds_tokyo_2011
105 cellline_nci60
106 odg_msk_2017
107 npc_nusingapore
108 nbl_amc_2012
109 nbl_ucologne_2015
110 nepc_wcm_2016
111 hnsc_mdanderson_2013
112 ov_tcga_pub
113 ov_tcga
114 skcm_vanderbilt_mskcc_2015
115 nsclc_tcga_broad_2016
116 paad_icgc
117 paad_qcmg_uq_2016
118 paad_tcga
119 paad_utsw_2015
120 panet_jhu_2011
121 thca_tcga_pub
122 es_dfarber_broad_2014
123 pcpg_tcga
124 thyroid_mskcc_2016
125 pcnsl_mayo_2015
126 prad_broad_2013
127 prad_broad
128 prad_fhcrc
129 prad_mskcc
130 prad_tcga_pub
131 prad_tcga
132 prad_mskcc_2014
133 prad_mskcc_cheny1_organoids_2014
134 prad_mich
135 hnc_mskcc_2016
136 nccrcc_genentech_2014
137 rms_nih_2014
138 sarc_mskcc
139 sarc_tcga
140 skcm_broad
141 skcm_tcga
142 skcm_yale
143 scco_mskcc
144 sclc_clcgp
145 sclc_jhu
146 sclc_ucologne_2015
147 stad_pfizer_uhongkong
148 stad_tcga_pub
149 stad_tcga
150 stad_utokyo
151 stad_uhongkong
152 stes_tcga_pub
153 tgct_tcga
154 tet_nci_2014
155 thym_tcga
156 thca_tcga
157 urcc_mskcc_2016
158 ucs_jhu_2014
159 ucs_tcga
160 ucec_tcga_pub
161 ucec_tcga
162 uvm_tcga
163 panet_arcnet_2017
164 past_dkfz_heidelberg_2013
name
1 Acinar Cell Carcinoma of the Pancreas (Johns Hopkins, J Pathol 2014)
2 Acute Myeloid Leukemia (TCGA, NEJM 2013)
3 Acute Myeloid Leukemia (TCGA, Provisional)
4 Adenoid Cystic Carcinoma (FMI, Am J Surg Pathl. 2014)
5 Adenoid Cystic Carcinoma (MDA, Clin Cancer Res 2015)
6 Adenoid Cystic Carcinoma (MSKCC, Nat Genet 2013)
7 Adenoid Cystic Carcinoma (Sanger/MDA, JCI 2013)
8 Adenoid Cystic Carcinoma of the Breast (MSKCC, J Pathol. 2015)
9 Adrenocortical Carcinoma (TCGA, Provisional)
10 Ampullary Carcinoma (Baylor College of Medicine, Cell Reports 2016)
11 Bladder Cancer (MSKCC, Eur Urol 2014)
12 Bladder Cancer (MSKCC, JCO 2013)
13 Bladder Cancer, Plasmacytoid Variant (MSKCC, Nat Genet 2016)
14 Bladder Urothelial Carcinoma (BGI, Nat Genet 2013)
15 Bladder Urothelial Carcinoma (Dana Farber & MSKCC, Cancer Discov 2014)
16 Bladder Urothelial Carcinoma (TCGA, Nature 2014)
17 Bladder Urothelial Carcinoma (TCGA, Provisional)
18 Brain Lower Grade Glioma (TCGA, Provisional)
19 Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)
20 Breast Invasive Carcinoma (British Columbia, Nature 2012)
21 Breast Invasive Carcinoma (Broad, Nature 2012)
22 Breast Invasive Carcinoma (Sanger, Nature 2012)
23 Breast Invasive Carcinoma (TCGA, Cell 2015)
24 Breast Invasive Carcinoma (TCGA, Nature 2012)
25 Breast Invasive Carcinoma (TCGA, Provisional)
26 Breast cancer patient xenografts (British Columbia, Nature 2014)
27 Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012)
28 Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA, Provisional)
29 Cholangiocarcinoma (National Cancer Centre of Singapore, Nat Genet 2013)
30 Cholangiocarcinoma (National University of Singapore, Nat Genet 2012)
31 Cholangiocarcinoma (TCGA, Provisional)
32 Chronic Lymphocytic Leukemia (Broad, Cell 2013)
33 Chronic Lymphocytic Leukemia (IUOPA, Nature 2015)
34 Clear Cell Renal Cell Carcinoma (U Tokyo, Nat Genet 2013)
35 Colorectal Adenocarcinoma (DFCI, Cell Reports 2016)
36 Colorectal Adenocarcinoma (Genentech, Nature 2012)
37 Colorectal Adenocarcinoma (TCGA, Nature 2012)
38 Colorectal Adenocarcinoma (TCGA, Provisional)
39 Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biol 2014)
40 Cutaneous T Cell Lymphoma (Columbia U, Nat Genet 2015)
41 Cutaneous squamous cell carcinoma (DFCI, Clin Cancer Res 2015)
42 Cystic Tumor of the Pancreas (Johns Hopkins, PNAS 2011
43 Desmoplastic Melanoma (Broad Institute, Nat Genet 2015)
44 Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012)
45 Esophageal Adenocarcinoma (Broad, Nat Genet 2013)
46 Esophageal Carcinoma (TCGA, Provisional)
47 Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014)
48 Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014)
49 Ewing Sarcoma (Institut Cuire, Cancer Discov 2014)
50 Gallbladder Carcinoma (Shanghai, Nat Genet 2014)
51 Gastric Adenocarcinoma (TMUCIH, PNAS 2015)
52 Genetic Characterization of NSCLC young adult patients ( University of Turin, Lung Cancer 2016)
53 Genetic Characterization of pretreatment melanoma tumors (UCLA, Cell 2016)
54 Genomic Hallmarks of Prostate Adenocarcinoma (CPC-GENE, Nature 2017)
55 Genomic Profile of Patients with Advanced Germ Cell Tumors (MSK, JCO 2016).
56 Glioblastoma (TCGA, Cell 2013)
57 Glioblastoma (TCGA, Nature 2008)
58 Glioblastoma Multiforme (TCGA, Provisional)
59 Head and Neck Squamous Cell Carcinoma (Broad, Science 2011)
60 Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011)
61 Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015)
62 Head and Neck Squamous Cell Carcinoma (TCGA, Provisional)
63 Hepatocellular Adenoma (Inserm, Cancer Cell 2014)
64 Hepatocellular Carcinomas (Inserm, Nat Genet 2015)
65 Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013)
66 Infant MLL-Rearranged Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015)
67 Insulinoma (Shanghai, Nat Commun 2013)
68 Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma. (Genome Res 2017)
69 Intrahepatic Cholangiocarcinoma (Johns Hopkins University, Nat Genet 2013)
70 Kidney Chromophobe (TCGA, Cancer Cell 2014)
71 Kidney Chromophobe (TCGA, Provisional)
72 Kidney Renal Clear Cell Carcinoma (BGI, Nat Genet 2012)
73 Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)
74 Kidney Renal Clear Cell Carcinoma (TCGA, Provisional)
75 Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional)
76 Liver Hepatocellular Carcinoma (AMC, Hepatology 2014)
77 Liver Hepatocellular Carcinoma (RIKEN, Nat Genet 2012)
78 Liver Hepatocellular Carcinoma (TCGA, Provisional)
79 Low-Grade Gliomas (UCSF, Science 2014)
80 Lung Adenocarcinoma (Broad, Cell 2012)
81 Lung Adenocarcinoma (MSKCC 2015)
82 Lung Adenocarcinoma (TCGA, Nature 2014)
83 Lung Adenocarcinoma (TCGA, Provisional)
84 Lung Adenocarcinoma (TSP, Nature 2008)
85 Lung Squamous Cell Carcinoma (TCGA, Nature 2012)
86 Lung Squamous Cell Carcinoma (TCGA, Provisional)
87 Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Provisional)
88 MSK-IMPACT Clinical Sequencing Cohort (MSKCC): Prostate Cancer
89 MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017)
90 Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nat Genet 2014)
91 Malignant Pleural Mesothelioma (NYU, Cancer Res 2015)
92 Mantle Cell Lymphoma (IDIBIPS, PNAS 2013)
93 Medulloblastoma (Broad, Nature 2012)
94 Medulloblastoma (ICGC, Nature 2012)
95 Medulloblastoma (PCGP, Nature 2012)
96 Medulloblastoma (Sickkids, Nature 2016)
97 Melanoma (Broad/Dana Farber, Nature 2012)
98 Merged Cohort of LGG and GBM (TCGA, Cell 2016)
99 Mesothelioma (TCGA, Provisional)
100 Metastatic Prostate Cancer, SU2C/PCF Dream Team (Robinson et al., Cell 2015)
101 Multiple Myeloma (Broad, Cancer Cell 2014)
102 Multiregion Sequencing of Clear Cell Renal Cell Carcinoma (IRC, Nat Genet 2014).
103 Mutational profiles of metastatic breast cancer (France, 2016)
104 Myelodysplasia (Tokyo, Nature 2011)
105 NCI-60 Cell Lines (NCI, Cancer Res. 2012)
106 NGS in Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas tumors (MSKCC, Neuro Oncol 2017)
107 Nasopharyngeal Carcinoma (Singapore, Nat Genet 2014)
108 Neuroblastoma (AMC Amsterdam, Nature 2012)
109 Neuroblastoma (Broad, Nat Genet 2013)
110 Neuroendocrine Prostate Cancer (Trento/Cornell/Broad 2016)
111 Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013)
112 Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011)
113 Ovarian Serous Cystadenocarcinoma (TCGA, Provisional)
114 PTEN loss of function alterations are associated with intrinsic resistance to BRAF inhibitors in metastatic melanoma (JCO Precision Oncology,2017)
115 Pan-Lung Cancer (TCGA, Nat Genet 2016)
116 Pancreatic Adenocarcinoma (ICGC, Nature 2012)
117 Pancreatic Adenocarcinoma (QCMG, Nature 2016)
118 Pancreatic Adenocarcinoma (TCGA, Provisional)
119 Pancreatic Cancer (UTSW, Nat Commun 2015)
120 Pancreatic Neuroendocrine Tumors (Johns Hopkins University, Science 2011)
121 Papillary Thyroid Carcinoma (TCGA, Cell 2014)
122 Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014)
123 Pheochromocytoma and Paraganglioma (TCGA, Provisional)
124 Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016)
125 Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)
126 Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
127 Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012)
128 Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016)
129 Prostate Adenocarcinoma (MSKCC, Cancer Cell 2010)
130 Prostate Adenocarcinoma (TCGA, Cell 2015)
131 Prostate Adenocarcinoma (TCGA, Provisional)
132 Prostate Adenocarcinoma CNA study (MSKCC, PNAS 2014)
133 Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014)
134 Prostate Adenocarcinoma, Metastatic (Michigan, Nature 2012)
135 Recurrent and Metastatic Head & Neck Cancer (JAMA Oncology, 2016)
136 Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014)
137 Rhabdomyosarcoma (NIH, Cancer Discov 2014)
138 Sarcoma (MSKCC/Broad, Nat Genet 2010)
139 Sarcoma (TCGA, Provisional)
140 Skin Cutaneous Melanoma (Broad, Cell 2012)
141 Skin Cutaneous Melanoma (TCGA, Provisional)
142 Skin Cutaneous Melanoma (Yale, Nat Genet 2012)
143 Small Cell Carcinoma of the Ovary (MSKCC, Nat Genet 2014)
144 Small Cell Lung Cancer (CLCGP, Nat Genet 2012)
145 Small Cell Lung Cancer (Johns Hopkins, Nat Genet 2012)
146 Small Cell Lung Cancer (U Cologne, Nature 2015)
147 Stomach Adenocarcinoma (Pfizer and UHK, Nat Genet 2014)
148 Stomach Adenocarcinoma (TCGA, Nature 2014)
149 Stomach Adenocarcinoma (TCGA, Provisional)
150 Stomach Adenocarcinoma (U Tokyo, Nat Genet 2014)
151 Stomach Adenocarcinoma (UHK, Nat Genet 2011)
152 TCGA data for Esophagus-Stomach Cancers (TCGA, Nature 2017)
153 Testicular Germ Cell Cancer (TCGA, Provisional)
154 Thymic Epithelial Tumors (NCI, Nat Genet 2014)
155 Thymoma (TCGA, Provisional)
156 Thyroid Carcinoma (TCGA, Provisional)
157 Unclassified Renal Cell Carcinoma (MSKCC 2016)
158 Uterine Carcinosarcoma (Johns Hopkins University, Nat Commun 2014)
159 Uterine Carcinosarcoma (TCGA, Provisional)
160 Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013)
161 Uterine Corpus Endometrial Carcinoma (TCGA, Provisional)
162 Uveal Melanoma (TCGA, Provisional)
163 Whole-Genome Sequencing of Pancreatic Neuroendocrine Tumors (Nature, 2017)
164 Whole-genome sequencing of pilocytic astrocytomasatic (Nat Genetics, 2013)
From: Hervé Pagès<mailto:hpages at fredhutch.org>
Sent: Friday, September 8, 2017 23:50
To: Arman Shahrisa<mailto:shahrisa.arman at hotmail.com>; bioc-devel<mailto:bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] How can I remove limit of row numbers that can be printed on console?
Hi Arman,
You're not saying what kind of object you're trying to print
but if it's a matrix or a data.frame then
print(x, max=nrow(x))
I'm not sure your users are going to find useful that your
function displays more than 99999 lines on their screen though...
Note that this more a general R programming question than a
Bioconductor question so the R-help mailing list would be a better
place to ask.
Cheers,
H.
On 09/08/2017 11:11 AM, Arman Shahrisa wrote:
>
> Hi everyone,
>
> How can I prevent the R from truncating the printed result on console? I have to
> print the output on console and I can�t use options(max.print = 10000) in my
> function. What else I can do?
>
> Sincerely
> Arman
>
>
> [[alternative HTML version deleted]]
>
>
>
> _______________________________________________
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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E-mail: hpages at fredhutch.org
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