Sorry, I didn’t think of that. I only added the lines to make my request clear.
Regards, Arman From: Lucas Schiffer<mailto:schiffer.lu...@gmail.com> Sent: Saturday, September 9, 2017 00:35 To: Arman Shahrisa<mailto:shahrisa.ar...@hotmail.com> Cc: Hervé Pagès<mailto:hpa...@fredhutch.org>; bioc-devel<mailto:bioc-devel@r-project.org> Subject: Re: [Bioc-devel] How can I remove limit of row numbers that can be printed on console? 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.ar...@hotmail.com<mailto:shahrisa.ar...@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:hpa...@fredhutch.org> Sent: Friday, September 8, 2017 23:50 To: Arman Shahrisa<mailto:shahrisa.ar...@hotmail.com>; bioc-devel<mailto:bioc-devel@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@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=w88PaHysSQzv2G0LUNhUYW4mqm4djlLrJm98kNP_CU8&s=4-dc114la3DQ_bTzLktj6fsnuEMWEgsKB7sOFut_c7M&e= -- 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: hpa...@fredhutch.org<mailto:hpa...@fredhutch.org> Phone: (206) 667-5791 Fax: (206) 667-1319 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
