Chapter 9. Documents 9-1
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Package 'Pinsplus'
Package ‘PINSPlus’ August 6, 2020 Encoding UTF-8 Type Package Title Clustering Algorithm for Data Integration and Disease Subtyping Version 2.0.5 Date 2020-08-06 Author Hung Nguyen, Bang Tran, Duc Tran and Tin Nguyen Maintainer Hung Nguyen <[email protected]> Description Provides a robust approach for omics data integration and disease subtyping. PIN- SPlus is fast and supports the analysis of large datasets with hundreds of thousands of sam- ples and features. The software automatically determines the optimal number of clus- ters and then partitions the samples in a way such that the results are ro- bust against noise and data perturbation (Nguyen et.al. (2019) <DOI: 10.1093/bioinformat- ics/bty1049>, Nguyen et.al. (2017)<DOI: 10.1101/gr.215129.116>). License LGPL Depends R (>= 2.10) Imports foreach, entropy , doParallel, matrixStats, Rcpp, RcppParallel, FNN, cluster, irlba, mclust RoxygenNote 7.1.0 Suggests knitr, rmarkdown, survival, markdown LinkingTo Rcpp, RcppArmadillo, RcppParallel VignetteBuilder knitr NeedsCompilation yes Repository CRAN Date/Publication 2020-08-06 21:20:02 UTC R topics documented: PINSPlus-package . .2 AML2004 . .2 KIRC ............................................3 PerturbationClustering . .4 SubtypingOmicsData . .9 1 2 AML2004 Index 13 PINSPlus-package Perturbation Clustering for data INtegration and disease Subtyping Description This package implements clustering algorithms proposed by Nguyen et al. (2017, 2019). Pertur- bation Clustering for data INtegration and disease Subtyping (PINS) is an approach for integraton of data and classification of diseases into various subtypes. PINS+ provides algorithms support- ing both single data type clustering and multi-omics data type. PINSPlus is an improved version of PINS by allowing users to customize the based clustering algorithm and perturbation methods. -
XMP SPECIFICATION PART 3 STORAGE in FILES Copyright © 2016 Adobe Systems Incorporated
XMP SPECIFICATION PART 3 STORAGE IN FILES Copyright © 2016 Adobe Systems Incorporated. All rights reserved. Adobe XMP Specification Part 3: Storage in Files NOTICE: All information contained herein is the property of Adobe Systems Incorporated. No part of this publication (whether in hardcopy or electronic form) may be reproduced or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written consent of Adobe Systems Incorporated. Adobe, the Adobe logo, Acrobat, Acrobat Distiller, Flash, FrameMaker, InDesign, Illustrator, Photoshop, PostScript, and the XMP logo are either registered trademarks or trademarks of Adobe Systems Incorporated in the United States and/or other countries. MS-DOS, Windows, and Windows NT are either registered trademarks or trademarks of Microsoft Corporation in the United States and/or other countries. Apple, Macintosh, Mac OS and QuickTime are trademarks of Apple Computer, Inc., registered in the United States and other countries. UNIX is a trademark in the United States and other countries, licensed exclusively through X/Open Company, Ltd. All other trademarks are the property of their respective owners. This publication and the information herein is furnished AS IS, is subject to change without notice, and should not be construed as a commitment by Adobe Systems Incorporated. Adobe Systems Incorporated assumes no responsibility or liability for any errors or inaccuracies, makes no warranty of any kind (express, implied, or statutory) with respect to this publication, and expressly disclaims any and all warranties of merchantability, fitness for particular purposes, and noninfringement of third party rights. Contents 1 Embedding XMP metadata in application files . -
Encapsulated Postscript File Format Specification
® Encapsulated PostScript File Format Specification ®® Adobe Developer Support Version 3.0 1 May 1992 Adobe Systems Incorporated Adobe Developer Technologies 345 Park Avenue San Jose, CA 95110 http://partners.adobe.com/ PN LPS5002 Copyright 1985–1988, 1990, 1992 by Adobe Systems Incorporated. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written consent of the publisher. Any software referred to herein is furnished under license and may only be used or copied in accordance with the terms of such license. PostScript is a registered trademark of Adobe Systems Incorporated. All instances of the name PostScript in the text are references to the PostScript language as defined by Adobe Systems Incorpo- rated unless otherwise stated. The name PostScript also is used as a product trademark for Adobe Sys- tems’ implementation of the PostScript language interpreter. Any references to a “PostScript printer,” a “PostScript file,” or a “PostScript driver” refer to printers, files, and driver programs (respectively) which are written in or support the PostScript language. The sentences in this book that use “PostScript language” as an adjective phrase are so constructed to rein- force that the name refers to the standard language definition as set forth by Adobe Systems Incorpo- rated. PostScript, the PostScript logo, Display PostScript, Adobe, the Adobe logo, Adobe Illustrator, Tran- Script, Carta, and Sonata are trademarks of Adobe Systems Incorporated registered in the U.S.A. and other countries. Adobe Garamond and Lithos are trademarks of Adobe Systems Incorporated. -
Lecture 2: Variables and Primitive Data Types
Lecture 2: Variables and Primitive Data Types MIT-AITI Kenya 2005 1 In this lecture, you will learn… • What a variable is – Types of variables – Naming of variables – Variable assignment • What a primitive data type is • Other data types (ex. String) MIT-Africa Internet Technology Initiative 2 ©2005 What is a Variable? • In basic algebra, variables are symbols that can represent values in formulas. • For example the variable x in the formula f(x)=x2+2 can represent any number value. • Similarly, variables in computer program are symbols for arbitrary data. MIT-Africa Internet Technology Initiative 3 ©2005 A Variable Analogy • Think of variables as an empty box that you can put values in. • We can label the box with a name like “Box X” and re-use it many times. • Can perform tasks on the box without caring about what’s inside: – “Move Box X to Shelf A” – “Put item Z in box” – “Open Box X” – “Remove contents from Box X” MIT-Africa Internet Technology Initiative 4 ©2005 Variables Types in Java • Variables in Java have a type. • The type defines what kinds of values a variable is allowed to store. • Think of a variable’s type as the size or shape of the empty box. • The variable x in f(x)=x2+2 is implicitly a number. • If x is a symbol representing the word “Fish”, the formula doesn’t make sense. MIT-Africa Internet Technology Initiative 5 ©2005 Java Types • Integer Types: – int: Most numbers you’ll deal with. – long: Big integers; science, finance, computing. – short: Small integers. -
Chapter 4 Variables and Data Types
PROG0101 Fundamentals of Programming PROG0101 FUNDAMENTALS OF PROGRAMMING Chapter 4 Variables and Data Types 1 PROG0101 Fundamentals of Programming Variables and Data Types Topics • Variables • Constants • Data types • Declaration 2 PROG0101 Fundamentals of Programming Variables and Data Types Variables • A symbol or name that stands for a value. • A variable is a value that can change. • Variables provide temporary storage for information that will be needed during the lifespan of the computer program (or application). 3 PROG0101 Fundamentals of Programming Variables and Data Types Variables Example: z = x + y • This is an example of programming expression. • x, y and z are variables. • Variables can represent numeric values, characters, character strings, or memory addresses. 4 PROG0101 Fundamentals of Programming Variables and Data Types Variables • Variables store everything in your program. • The purpose of any useful program is to modify variables. • In a program every, variable has: – Name (Identifier) – Data Type – Size – Value 5 PROG0101 Fundamentals of Programming Variables and Data Types Types of Variable • There are two types of variables: – Local variable – Global variable 6 PROG0101 Fundamentals of Programming Variables and Data Types Types of Variable • Local variables are those that are in scope within a specific part of the program (function, procedure, method, or subroutine, depending on the programming language employed). • Global variables are those that are in scope for the duration of the programs execution. They can be accessed by any part of the program, and are read- write for all statements that access them. 7 PROG0101 Fundamentals of Programming Variables and Data Types Types of Variable MAIN PROGRAM Subroutine Global Variables Local Variable 8 PROG0101 Fundamentals of Programming Variables and Data Types Rules in Naming a Variable • There a certain rules in naming variables (identifier). -
Web Compatible SAS/GRAPH Output the Easy
Web Compatible SAS/GRAPH® Output the Easy Way Ahsan Ullah, Pinkerton Computer Consultants, Inc., Alexandria, VA ABSTRACT • Proper use of colors is a must to make the image attractive. • (TM) This paper describes some concepts and analyses required If there is an option to print the image, a PostScript to create SAS/GRAPH images for use in WEB pages. It file needs to be tagged along with the image which will deals with an automated SAS/AF® Frame system designed to keep the usual form of the printed output create and print a number of graphs and produce suitable • In order to print a hard copy of the graph from the graph image files for inclusion on WEB pages. Topics internet, a PostScript color or black and white with discussed include drill-down design, programming minimum of 0.5 X 0.5 inch margin should be selected. (TM) techniques for creating GIF files, and the creation of custom Most Hewlett Packard printers satisfy the SAS Device Drivers. requirements. INTRODUCTION A user-friendly SAS/AF Frame system needs to be created to perform the following functions: • Interactive or batch process to create images. SAS software is a major leader in information and • Support the selection of device drivers to print or management systems. It has powerful features that support transport postscript or GIF file. the creation of customized hard copy output that includes • both data and graphic output. Until now, SAS custom graphs Automatically add HTML code to create Web-ready could not take their place in the Web world because of: graph images • Sophistication of SAS custom graphs • True portability across platforms Device Drivers • Interactive way to create and process graphs A GIF device driver is needed for SAS software to create a GIF Image file of the graph. -
The Art of the Javascript Metaobject Protocol
The Art Of The Javascript Metaobject Protocol enough?Humphrey Ephraim never recalculate remains giddying: any precentorship she expostulated exasperated her nuggars west, is brocade Gus consultative too around-the-clock? and unbloody If dog-cheapsycophantical and or secularly, norman Partha how slicked usually is volatilisingPenrod? his nomadism distresses acceptedly or interlacing Card, and send an email to a recipient with. On Auslegung auf are Schallabstrahlung download the Aerodynamik von modernen Flugtriebwerken. This poll i send a naming convention, the art of metaobject protocol for the corresponding to. What might happen, for support, if you should load monkeypatched code in one ruby thread? What Hooks does Ruby have for Metaprogramming? Sass, less, stylus, aura, etc. If it finds one, it calls that method and passes itself as value object. What bin this optimization achieve? JRuby and the psd. Towards a new model of abstraction in software engineering. Buy Online in Aruba at aruba. The current run step approach is: Checkpoint. Python object room to provide usable string representations of hydrogen, one used for debugging and logging, another for presentation to end users. Method handles can we be used to implement polymorphic inline caches. Mop is not the metaobject? Rails is a nicely designed web framework. Get two FREE Books of character Moment sampler! The download the number IS still thought. This proxy therefore behaves equivalently to the card dispatch function, and no methods will be called on the proxy dispatcher before but real dispatcher is available. While desertcart makes reasonable efforts to children show products available in your kid, some items may be cancelled if funny are prohibited for import in Aruba. -
Julia's Efficient Algorithm for Subtyping Unions and Covariant
Julia’s Efficient Algorithm for Subtyping Unions and Covariant Tuples Benjamin Chung Northeastern University, Boston, MA, USA [email protected] Francesco Zappa Nardelli Inria of Paris, Paris, France [email protected] Jan Vitek Northeastern University, Boston, MA, USA Czech Technical University in Prague, Czech Republic [email protected] Abstract The Julia programming language supports multiple dispatch and provides a rich type annotation language to specify method applicability. When multiple methods are applicable for a given call, Julia relies on subtyping between method signatures to pick the correct method to invoke. Julia’s subtyping algorithm is surprisingly complex, and determining whether it is correct remains an open question. In this paper, we focus on one piece of this problem: the interaction between union types and covariant tuples. Previous work normalized unions inside tuples to disjunctive normal form. However, this strategy has two drawbacks: complex type signatures induce space explosion, and interference between normalization and other features of Julia’s type system. In this paper, we describe the algorithm that Julia uses to compute subtyping between tuples and unions – an algorithm that is immune to space explosion and plays well with other features of the language. We prove this algorithm correct and complete against a semantic-subtyping denotational model in Coq. 2012 ACM Subject Classification Theory of computation → Type theory Keywords and phrases Type systems, Subtyping, Union types Digital Object Identifier 10.4230/LIPIcs.ECOOP.2019.24 Category Pearl Supplement Material ECOOP 2019 Artifact Evaluation approved artifact available at https://dx.doi.org/10.4230/DARTS.5.2.8 Acknowledgements The authors thank Jiahao Chen for starting us down the path of understanding Julia, and Jeff Bezanson for coming up with Julia’s subtyping algorithm. -
Does Personality Matter? Temperament and Character Dimensions in Panic Subtypes
325 Arch Neuropsychiatry 2018;55:325−329 RESEARCH ARTICLE https://doi.org/10.5152/npa.2017.20576 Does Personality Matter? Temperament and Character Dimensions in Panic Subtypes Antonio BRUNO1 , Maria Rosaria Anna MUSCATELLO1 , Gianluca PANDOLFO1 , Giulia LA CIURA1 , Diego QUATTRONE2 , Giuseppe SCIMECA1 , Carmela MENTO1 , Rocco A. ZOCCALI1 1Department of Psychiatry, University of Messina, Messina, Italy 2MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, United Kingdom ABSTRACT Introduction: Symptomatic heterogeneity in the clinical presentation of and 12.78% of the total variance. Correlations analyses showed that Panic Disorder (PD) has lead to several attempts to identify PD subtypes; only “Somato-dissociative” factor was significantly correlated with however, no studies investigated the association between temperament T.C.I. “Self-directedness” (p<0.0001) and “Cooperativeness” (p=0.009) and character dimensions and PD subtypes. The study was aimed to variables. Results from the regression analysis indicate that the predictor verify whether personality traits were differentially related to distinct models account for 33.3% and 24.7% of the total variance respectively symptom dimensions. in “Somatic-dissociative” (p<0.0001) and “Cardiologic” (p=0.007) factors, while they do not show statistically significant effects on “Respiratory” Methods: Seventy-four patients with PD were assessed by the factor (p=0.222). After performing stepwise regression analysis, “Self- Mini-International Neuropsychiatric Interview (M.I.N.I.), and the directedness” resulted the unique predictor of “Somato-dissociative” Temperament and Character Inventory (T.C.I.). Thirteen panic symptoms factor (R²=0.186; β=-0.432; t=-4.061; p<0.0001). from the M.I.N.I. -
Making TIFF Files from Drawing, Word Processing, Powerpoint And
Making TIFF and EPS files from Drawing, Word Processing, PowerPoint and Graphing Programs In the worlds of electronic publishing and video production programs, the need for TIFF or EPS formatted files is a necessity. Unfortunately, most of the imaging work done in research for presen- tation is done in PowerPoint, and this format simply cannot be used in most situations for these three ends. Files can be generally be saved or exported (by using either Save As or Export under File) into TIFF, PICT or JPEG files from PowerPoint, drawing, word processing and graphing programs—all called vector programs—but the results are often poor in resolution (in Photoshop these are shown as having a resolution of 72dpi when opening the Image Size dialogue box: under Image on the menu select Image Size). Here are four ways to save as TIFF (generally the way in which image files are saved) or EPS (gen- erally the way in which files are saved which contain lines or text): Option 1. Use the Program’s Save As or Export option. If it exists, use the Export or Save As option in your vector program. This only works well when a dialogue box appears so that specific values for height, width and resolution can be typed in (as in the programs Canvas and CorelDraw). Anti-aliasing should be checked. Resolution values of 300 dots per inch or pixels per inch is for images, 600 dpi is for images with text and 1200 dpi is for text, graphs and drawings. If no dialogue box exists to type in these values, go to option 2 - 4. -
Plain Text & Character Encoding
Journal of eScience Librarianship Volume 10 Issue 3 Data Curation in Practice Article 12 2021-08-11 Plain Text & Character Encoding: A Primer for Data Curators Seth Erickson Pennsylvania State University Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/jeslib Part of the Scholarly Communication Commons, and the Scholarly Publishing Commons Repository Citation Erickson S. Plain Text & Character Encoding: A Primer for Data Curators. Journal of eScience Librarianship 2021;10(3): e1211. https://doi.org/10.7191/jeslib.2021.1211. Retrieved from https://escholarship.umassmed.edu/jeslib/vol10/iss3/12 Creative Commons License This work is licensed under a Creative Commons Attribution 4.0 License. This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in Journal of eScience Librarianship by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. ISSN 2161-3974 JeSLIB 2021; 10(3): e1211 https://doi.org/10.7191/jeslib.2021.1211 Full-Length Paper Plain Text & Character Encoding: A Primer for Data Curators Seth Erickson The Pennsylvania State University, University Park, PA, USA Abstract Plain text data consists of a sequence of encoded characters or “code points” from a given standard such as the Unicode Standard. Some of the most common file formats for digital data used in eScience (CSV, XML, and JSON, for example) are built atop plain text standards. Plain text representations of digital data are often preferred because plain text formats are relatively stable, and they facilitate reuse and interoperability. -
Software II: Principles of Programming Languages
Software II: Principles of Programming Languages Lecture 6 – Data Types Some Basic Definitions • A data type defines a collection of data objects and a set of predefined operations on those objects • A descriptor is the collection of the attributes of a variable • An object represents an instance of a user- defined (abstract data) type • One design issue for all data types: What operations are defined and how are they specified? Primitive Data Types • Almost all programming languages provide a set of primitive data types • Primitive data types: Those not defined in terms of other data types • Some primitive data types are merely reflections of the hardware • Others require only a little non-hardware support for their implementation The Integer Data Type • Almost always an exact reflection of the hardware so the mapping is trivial • There may be as many as eight different integer types in a language • Java’s signed integer sizes: byte , short , int , long The Floating Point Data Type • Model real numbers, but only as approximations • Languages for scientific use support at least two floating-point types (e.g., float and double ; sometimes more • Usually exactly like the hardware, but not always • IEEE Floating-Point Standard 754 Complex Data Type • Some languages support a complex type, e.g., C99, Fortran, and Python • Each value consists of two floats, the real part and the imaginary part • Literal form real component – (in Fortran: (7, 3) imaginary – (in Python): (7 + 3j) component The Decimal Data Type • For business applications (money)