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‎R/SCRABBLE_0.0.1_R.Rcheck/00_pkg_src/SCRABBLE/DESCRIPTION

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Package: SCRABBLE
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Type: Package
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Title: Impute scRNAseq data method
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Version: 0.0.1
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Author: Tao Peng
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Maintainer: The package maintainer Tao Peng <software.github@gmail.com>
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Description: SCRABBLE imputes drop-out data by optimizing an objective function
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that consists of three terms. The first term ensures that imputed values for
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genes with nonzero expression remain as close to their original values as possible,
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thus minimizing unwanted bias towards expressed genes. The second term ensures the
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rank of the imputed data matrix to be as small as possible. The rationale is that
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we only expect a limited number of distinct cell types in the samples. The third term
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operates on the bulk RNA-Seq data. It ensures consistency between the average gene
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expression of the aggregated imputed data and the average gene expression of the bulk
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RNA-Seq data. We developed a convex optimization algorithm to minimize the objective function.
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License: GPL-3
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Encoding: UTF-8
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Depends: R(>= 3.3)
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LazyData: true
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Imports: Rcpp (>= 0.12.13), rARPACK, pracma, ggplot2, RColorBrewer,
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reshape2, gridExtra
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LinkingTo: Rcpp, RcppEigen, gridExtra
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RoxygenNote: 6.1.1
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Suggests: knitr,rmarkdown,BiocStyle
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VignetteBuilder: knitr
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Built: R 3.5.1; x86_64-redhat-linux-gnu; 2019-03-03 21:45:35 UTC; unix

‎R/SCRABBLE_0.0.1_R.Rcheck/00_pkg_src/SCRABBLE/INDEX

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scrabble Runs SCRABBLE

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‎R/SCRABBLE_0.0.1_R.Rcheck/00_pkg_src/SCRABBLE/NAMESPACE

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#exportPattern("^[[:alpha:]]+")
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importFrom(Rcpp, evalCpp)
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useDynLib(SCRABBLE, .registration = TRUE)
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export(scrabble)
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export(plot_data)
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import(Rcpp)
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import(rARPACK)
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import(pracma)
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import(ggplot2)
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import(RColorBrewer)
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import(reshape2)
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import(gridExtra)

‎R/SCRABBLE_0.0.1_R.Rcheck/00_pkg_src/SCRABBLE/R/SCRABBLE

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# File share/R/nspackloader.R
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# Part of the R package, http://www.R-project.org
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#
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# Copyright (C) 1995-2012 The R Core Team
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; either version 2 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# A copy of the GNU General Public License is available at
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# http://www.r-project.org/Licenses/
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local({
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info <- loadingNamespaceInfo()
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pkg <- info$pkgname
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ns <- .getNamespace(as.name(pkg))
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if (is.null(ns))
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stop("cannot find namespace environment for ", pkg, domain = NA);
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dbbase <- file.path(info$libname, pkg, "R", pkg)
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lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
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})

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‎R/SCRABBLE_0.0.1_R.Rcheck/00_pkg_src/SCRABBLE/help/AnIndex

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scrabble SCRABBLE

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‎R/SCRABBLE_0.0.1_R.Rcheck/00_pkg_src/SCRABBLE/html/00Index.html

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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head><title>R: Impute scRNAseq data method</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<link rel="stylesheet" type="text/css" href="R.css" />
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</head><body>
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<h1> Impute scRNAseq data method
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<img class="toplogo" src="../../../doc/html/Rlogo.svg" alt="[R logo]" />
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</h1>
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<hr/>
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<div style="text-align: center;">
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<a href="../../../doc/html/packages.html"><img class="arrow" src="../../../doc/html/left.jpg" alt="[Up]" /></a>
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<a href="../../../doc/html/index.html"><img class="arrow" src="../../../doc/html/up.jpg" alt="[Top]" /></a>
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</div><h2>Documentation for package &lsquo;SCRABBLE&rsquo; version 0.0.1</h2>
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<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
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</ul>
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<h2>Help Pages</h2>
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<table width="100%">
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<tr><td style="width: 25%;"><a href="SCRABBLE.html">scrabble</a></td>
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<td>Runs SCRABBLE</td></tr>
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</table>
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</body></html>

‎R/SCRABBLE_0.0.1_R.Rcheck/00_pkg_src/SCRABBLE/html/R.css

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}
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‎R/SCRABBLE_0.0.1_R.Rcheck/00_pkg_src/SCRABBLE/html/SCRABBLE.html

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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: Runs SCRABBLE</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<link rel="stylesheet" type="text/css" href="R.css" />
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</head><body>
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<table width="100%" summary="page for scrabble {SCRABBLE}"><tr><td>scrabble {SCRABBLE}</td><td style="text-align: right;">R Documentation</td></tr></table>
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<h2>Runs SCRABBLE</h2>
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<h3>Description</h3>
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<p>SCRABBLE imputes drop-out data by optimizing an objective function that consists of three terms.
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The first term ensures that imputed values for genes with nonzero expression remain as close to their
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original values as possible, thus minimizing unwanted bias towards expressed genes. The second term ensures
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the rank of the imputed data matrix to be as small as possible. The rationale is that we only expect a
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limited number of distinct cell types in the samples. The third term operates on the bulk RNA-Seq data.
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It ensures consistency between the average gene expression of the aggregated imputed data and the
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average gene expression of the bulk RNA-Seq data. We developed 58 a convex optimization algorithm to minimize
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the objective function.
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</p>
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<h3>Usage</h3>
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<pre>
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scrabble(data, parameter, nIter = 60, error_out_threshold = 1e-07,
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nIter_inner = 100, error_inner_threshold = 1e-05)
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</pre>
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<h3>Arguments</h3>
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<table summary="R argblock">
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<tr valign="top"><td><code>data</code></td>
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<td>
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<p>the input data list. The input
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data is a list of two datasets, scRNAseq and bulk RNAseq.</p>
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</td></tr>
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<tr valign="top"><td><code>parameter</code></td>
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<td>
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<p>the vector of parameters. The first parameter is the value of alpha in the mathematical model
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, the second one is the value of beta in the mathematical model.</p>
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</td></tr>
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<tr valign="top"><td><code>nIter</code></td>
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<td>
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<p>the maximum iterations, the default is 60.</p>
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</td></tr>
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<tr valign="top"><td><code>error_out_threshold</code></td>
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<td>
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<p>the threshold of the error between the current imputed matrix and the previous one.
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Default is 1e-5.</p>
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</td></tr>
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<tr valign="top"><td><code>nIter_inner</code></td>
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<td>
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<p>the maximum interations of calculating the sub-optimization problem. Default is 60.</p>
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</td></tr>
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<tr valign="top"><td><code>error_inner_threshold</code></td>
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<td>
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<p>the threshold of the error between the current updated matrix and the previous one.
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Default is 1e-5.</p>
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</td></tr>
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</table>
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<h3>Value</h3>
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<p>A data matrix with the same size of the input scRNAseq data
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</p>
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<h3>Examples</h3>
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<pre>
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# Set up the parameter used in SCRABBLE
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parameter &lt;- c(1, 1e-6, 1e-4)
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# Run SCRABLE
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result &lt;- scrabble(data,parameter = parameter)
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</pre>
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<hr /><div style="text-align: center;">[Package <em>SCRABBLE</em> version 0.0.1 <a href="00Index.html">Index</a>]</div>
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</body></html>

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‎R/SCRABBLE_0.0.1_R.Rcheck/00check.log

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* using log directory ‘/mnt/isilon/tan_lab/pengt/Documents/Chop/SCRABBLE_github/SCRABBLE/R/SCRABBLE_0.0.1_R.Rcheck’
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* using R version 3.5.1 (2018-07-02)
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* using platform: x86_64-redhat-linux-gnu (64-bit)
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* using session charset: UTF-8
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* checking package directory ... ERROR
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package directory ‘/mnt/isilon/tan_lab/pengt/Documents/Chop/SCRABBLE_github/SCRABBLE/R/SCRABBLE_0.0.1_R.Rcheck/00_pkg_src/SCRABBLE_0.0.1_R’ does not exist
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* DONE
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Status: 1 ERROR

‎R/SCRABBLE_0.0.1_R_x86_64-redhat-linux-gnu.Rcheck/00_pkg_src/SCRABBLE/DESCRIPTION

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Package: SCRABBLE
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Type: Package
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Title: Impute scRNAseq data method
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Version: 0.0.1
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Author: Tao Peng
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Maintainer: The package maintainer Tao Peng <software.github@gmail.com>
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Description: SCRABBLE imputes drop-out data by optimizing an objective function
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that consists of three terms. The first term ensures that imputed values for
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genes with nonzero expression remain as close to their original values as possible,
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thus minimizing unwanted bias towards expressed genes. The second term ensures the
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rank of the imputed data matrix to be as small as possible. The rationale is that
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we only expect a limited number of distinct cell types in the samples. The third term
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operates on the bulk RNA-Seq data. It ensures consistency between the average gene
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expression of the aggregated imputed data and the average gene expression of the bulk
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RNA-Seq data. We developed a convex optimization algorithm to minimize the objective function.
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License: GPL-3
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Encoding: UTF-8
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Depends: R(>= 3.3)
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LazyData: true
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Imports: Rcpp (>= 0.12.13), rARPACK, pracma, ggplot2, RColorBrewer,
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reshape2, gridExtra
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LinkingTo: Rcpp, RcppEigen, gridExtra
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RoxygenNote: 6.1.1
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Suggests: knitr,rmarkdown,BiocStyle
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VignetteBuilder: knitr
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Built: R 3.5.1; x86_64-redhat-linux-gnu; 2019-03-04 01:23:28 UTC; unix

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scrabble Runs SCRABBLE

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#exportPattern("^[[:alpha:]]+")
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importFrom(Rcpp, evalCpp)
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useDynLib(SCRABBLE, .registration = TRUE)
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export(scrabble)
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export(plot_data)
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import(Rcpp)
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import(rARPACK)
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import(pracma)
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import(ggplot2)
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import(RColorBrewer)
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import(reshape2)
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import(gridExtra)

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# File share/R/nspackloader.R
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# Part of the R package, http://www.R-project.org
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#
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# Copyright (C) 1995-2012 The R Core Team
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; either version 2 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# A copy of the GNU General Public License is available at
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# http://www.r-project.org/Licenses/
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local({
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info <- loadingNamespaceInfo()
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pkg <- info$pkgname
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ns <- .getNamespace(as.name(pkg))
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if (is.null(ns))
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stop("cannot find namespace environment for ", pkg, domain = NA);
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dbbase <- file.path(info$libname, pkg, "R", pkg)
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lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
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})

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scrabble SCRABBLE

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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head><title>R: Impute scRNAseq data method</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<link rel="stylesheet" type="text/css" href="R.css" />
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</head><body>
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<h1> Impute scRNAseq data method
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<img class="toplogo" src="../../../doc/html/Rlogo.svg" alt="[R logo]" />
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</h1>
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<hr/>
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<div style="text-align: center;">
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<a href="../../../doc/html/packages.html"><img class="arrow" src="../../../doc/html/left.jpg" alt="[Up]" /></a>
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<a href="../../../doc/html/index.html"><img class="arrow" src="../../../doc/html/up.jpg" alt="[Top]" /></a>
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</div><h2>Documentation for package &lsquo;SCRABBLE&rsquo; version 0.0.1</h2>
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<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
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</ul>
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<h2>Help Pages</h2>
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<table width="100%">
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<tr><td style="width: 25%;"><a href="SCRABBLE.html">scrabble</a></td>
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<td>Runs SCRABBLE</td></tr>
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</table>
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</body></html>

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