ViewPagodaApp

ViewPagodaApp-class


This ROOK application class enables communication with the client-side ExtJS framework and Inchlib HTML5 canvas libraries to create the graphical user interface for PAGODA
Refer to the code in <code><a rd-options="" href="/link/make.pagoda.app?package=scde&version=2.0.0" data-mini-rdoc="scde::make.pagoda.app">make.pagoda.app</a></code> for usage example


The scde package implements a set of statistical methods for
analyzing single-cell RNA-seq data. scde fits individual error models for
single-cell RNA-seq measurements. These models can then be used for assessment
of differential expression between groups of cells, as well as other types of
analysis. The scde package also contains the pagoda framework which applies
pathway and gene set overdispersion analysis to identify and characterize
putative cell subpopulations based on transcriptional signatures. The overall
approach to the differential expression analysis is detailed in the following
publication: "Bayesian approach to single-cell differential expression
analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi:
10.1038/nmeth.2967). The overall approach to subpopulation identification and
characterization is detailed in the following pre-print: "Characterizing
transcriptional heterogeneity through pathway and gene set overdispersion
analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F,
Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).

Peter Kharchenko

scde

Single Cell Differential Expression

ViewPagodaApp-class function

 <dl>
<dt><code>results</code></dt><dd>Output of the pathway clustering and redundancy reduction</dd> <dt><code>genes</code></dt><dd>List of genes to display in the Detailed clustering panel</dd> <dt><code>mat</code></dt><dd>Matrix of posterior mode count estimates</dd> <dt><code>matw</code></dt><dd>Matrix of weights associated with each estimate in <code>mat</code></dd> <dt><code>goenv</code></dt><dd>Gene set list as an environment</dd> <dt><code>renv</code></dt><dd>Global environment</dd> <dt><code>name</code></dt><dd>Name of the application page; for display as the page title</dd> <dt><code>trim</code></dt><dd>Trim quantity used for Winsorization for visualization</dd> <dt><code>batch</code></dt><dd>Any batch or other known confounders to be included in the visualization as a column color track</dd> </dl>

Fields


This ROOK application class enables communication with the client-side ExtJS framework and Inchlib HTML5 canvas libraries to create the graphical user interface for PAGODA
Refer to the code in <code><a rd-options='' href='make.pagoda.app'>make.pagoda.app</a></code> for usage example


ViewPagodaApp-class: A Reference Class to represent the PAGODA application

Description

Arguments

Fields