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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CADD score has limited clinical validity for the identification of pathogenic variants in noncoding regions in a hereditary cancer panel.
Cheryl A. Mather,Sean D. Mooney,Stephen J. Salipante,Sheena M. Scroggins,David Wu,Colin C. Pritchard,Brian H. Shirts +6 more
TL;DR: Focused in silico scoring systems with much higher predictive value will be necessary for clinical genomic applications and no individual variants could be identified as plausibly causative among the rare intronic variants with the highest scores.
Journal ArticleDOI
Treatment default amongst patients with tuberculosis in urban Morocco: predicting and explaining default and post-default sputum smear and drug susceptibility results.
Imad Cherkaoui,Radia Sabouni,Iraqi Ghali,Darya Kizub,Alexander C. Billioux,Kenza Bennani,Jamal Eddine Bourkadi,Abderrahmane Benmamoun,Ouafae Lahlou,Rajae El Aouad,Kelly E. Dooley +10 more
TL;DR: The causes of default from TB treatment were explored through synthesis of qualitative and quantitative data from patients and health professionals, and a scoring tool with high sensitivity and specificity to predict default was developed.
Journal ArticleDOI
Single-cell differences in matrix gene expression do not predict matrix deposition.
Allison Cote,Claire M. McLeod,Claire M. McLeod,Megan J. Farrell,Patrick D. McClanahan,Margaret C. Dunagin,Arjun Raj,Robert L. Mauck,Robert L. Mauck +8 more
TL;DR: These quantitative analyses suggest that sorting subpopulations based on these markers would only marginally enrich the progenitor population for ‘superior' MSCs, and suggest that instantaneous mRNA abundance of canonical markers is tenuously linked to the chondrogenic phenotype at the single-cell level.
Journal ArticleDOI
Increased Levels of Antigen-Bound β-Amyloid Autoantibodies in Serum and Cerebrospinal Fluid of Alzheimer’s Disease Patients
Madalina Maftei,Franka Thurm,Franka Thurm,Franka Thurm,Cathrin Schnack,Hayrettin Tumani,Markus Otto,Thomas Elbert,Iris-Tatjana Kolassa,Iris-Tatjana Kolassa,Michael Przybylski,Marilena Manea,Christine A. F. von Arnim +12 more
TL;DR: The application of a new sandwich enzyme-linked immunosorbent assay (ELISA) for the determination of antigen-bound Aβ-autoantibodies (intact A β-IgG immune complexes) in serum and cerebrospinal fluid (CSF) of a total number of 112 AD patients and age- and gender-matched control subjects suggests a contribution of IgG-type autoantibodied to Aβ clearance in vivo and an increased immune response in AD.
Journal ArticleDOI
Mid-upper arm circumference as a screening tool for identifying children with obesity: a 12-country study
J-P Chaput,Peter T. Katzmarzyk,Joel D. Barnes,Mikael Fogelholm,Gang Hu,Rebecca Kuriyan,Anura V Kurpad,Estelle V. Lambert,Carol Maher,José Maia,Victor Matsudo,Tim Olds,Vincent Onywera,Olga L. Sarmiento,Martyn Standage,Catrine Tudor-Locke,Pei Zhao,Mark S. Tremblay +17 more
TL;DR: No studies have examined if mid‐upper arm circumference (MUAC) can be an alternative screening tool for obesity in an international sample of children differing widely in levels of human development.
References
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