Do realize that this email list goes out to hundreds of people and hundreds of lines of output are a bit like receiving spam.
> On Sep 8, 2017, at 16:01, Arman Shahrisa <shahrisa.arman at hotmail.com> wrote:
>
> 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 <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 <mailto:hpages at fredhutch.org>>
> Sent: Friday, September 8, 2017 23:50
> To: Arman Shahrisa<mailto:shahrisa.arman at hotmail.com <mailto:shahrisa.arman at hotmail.com>>; bioc-devel<mailto:bioc-devel at r-project.org <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]]
>>
>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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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
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
>
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>
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