pROC: an open-source package for R and S+ to analyze and compare ROC curves
Xavier Robin,Natacha Turck,Alexandre Hainard,Natalia Tiberti,Frédérique Lisacek,Jean-Charles Sanchez,Markus Müller +6 more
TLDR
pROC as mentioned in this paper is a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface.Abstract:
Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface. With data previously imported into the R or S+ environment, the pROC package builds ROC curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing ROC curves. Intermediary and final results are visualised in user-friendly interfaces. A case study based on published clinical and biomarker data shows how to perform a typical ROC analysis with pROC. pROC is a package for R and S+ specifically dedicated to ROC analysis. It proposes multiple statistical tests to compare ROC curves, and in particular partial areas under the curve, allowing proper ROC interpretation. pROC is available in two versions: in the R programming language or with a graphical user interface in the S+ statistical software. It is accessible at http://expasy.org/tools/pROC/
under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation.read more
Citations
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Journal ArticleDOI
Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation.
Kaija-Leena Kolho,Katri Korpela,Tytti Jaakkola,Madharasi V A Pichai,Erwin G. Zoetendal,Anne Salonen,Willem M. de Vos +6 more
TL;DR: Intestinal microbiota represents a potential biomarker for correlating the level of inflammation and therapeutic responses to be further validated.
Journal ArticleDOI
Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation
Rasmus Siersbæk,Jesper Grud Skat Madsen,Biola M. Javierre,Ronni Nielsen,Emilie Kristine Bagge,Jonathan Cairns,Steven W. Wingett,Sofie Traynor,Mikhail Spivakov,Peter Fraser,Peter Fraser,Susanne Mandrup +11 more
TL;DR: Intriguingly, formation of loops connecting activated enhancers and promoters is also associated with extensive recruitment of corepressors such as NCoR and HDACs, indicating that this class of coregulators may play a previously unrecognized role during enhancer activation.
Journal ArticleDOI
Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer
Ludovic Barault,Alessio Amatu,Giulia Siravegna,Agostino Ponzetti,Sebastian Moran,Andrea Cassingena,Benedetta Mussolin,Chiara Falcomatà,Alexandra M. Binder,Carmen Cristiano,Daniele Oddo,Simonetta Guarrera,Carlotta Cancelliere,Sara Bustreo,Katia Bencardino,Sean K. Maden,Alice Vanzati,Patrizia Zavattari,Giuseppe Matullo,Mauro Truini,William M. Grady,Patrizia Racca,Karin B. Michels,Salvatore Siena,Manel Esteller,Alberto Bardelli,Andrea Sartore-Bianchi,Federica Di Nicolantonio +27 more
TL;DR: This five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens.
Journal ArticleDOI
Noninvasive Early Identification of Therapeutic Benefit from Immune Checkpoint Inhibition.
Barzin Y. Nabet,Mohammad Shahrokh Esfahani,Everett J. Moding,Emily G. Hamilton,Jacob J. Chabon,Hira Rizvi,Chloé B. Steen,Aadel A. Chaudhuri,Chih Long Liu,Angela B. Hui,Diego Almanza,Henning Stehr,Linda Gojenola,Rene F. Bonilla,Michael C. Jin,Young-Jun Jeon,Young-Jun Jeon,Diane Tseng,Cailian Liu,Taha Merghoub,Joel W. Neal,Heather A. Wakelee,Sukhmani K. Padda,Kavitha Ramchandran,Millie Das,Millie Das,Andrew J. Plodkowski,Christopher H. Yoo,Emily Chen,Ryan B. Ko,Aaron M. Newman,Matthew D. Hellmann,Ash A. Alizadeh,Maximilian Diehn +33 more
TL;DR: It is demonstrated that pre-treatment circulating tumor DNA (ctDNA) and peripheral CD8 T cell levels are independently associated with DCB and that ctDNA dynamics after a single infusion can aid in identification of patients who will achieve durable clinical benefit (DCB).
Journal ArticleDOI
Clinical and Metabolic Characterization of Lean Caucasian Subjects With Non-alcoholic Fatty Liver
Alexandra Feldman,Sebastian K. Eder,Thomas K. Felder,Lyudmyla Kedenko,Bernhard Paulweber,Andreas Stadlmayr,Ursula Huber-Schönauer,David Niederseer,Felix Stickel,Simon Auer,Elisabeth Haschke-Becher,Wolfgang Patsch,Christian Datz,Elmar Aigner +13 more
TL;DR: Lean subjects with evidence of NAFLD have clinically relevant impaired glucose tolerance, low adiponectin concentrations and a distinct metabolite profile with an increased rate of PNPLA3 risk allele carriage.
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