mol_quick_analysis

Quick molecule analysis and report generation

Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.

Shixiang Wang

UCSCXenaShiny

Interactive Analysis of UCSC Xena Data

Shensuo Li

Yi Xiong

Longfei Zhao

Kai Gu

Yin Li

Fei Zhao

mol_quick_analysis function

<dl><dt>molecule</dt>
<dd>a molecular identifier (e.g., "TP53") or a formula specifying
genomic signature (<code>"TP53 + 2 * KRAS - 1.3 * PTEN"</code>).</dd>
<dt>data_type</dt>
<dd>data type. Can be one of "mRNA", "transcript", "protein",
"mutation", "cnv", "methylation", "miRNA".</dd>
<dt>out_dir</dt>
<dd>path to save analysis result and report, default is '.'</dd>
<dt>out_report</dt>
<dd>logical value wheather to generate html report</dd></dl>

Arguments

Quick molecule analysis and report generation — mol_quick_analysis

<dl>

<dt>molecule</dt>
<dd>a molecular identifier (e.g., "TP53") or a formula specifying
genomic signature (<code>"TP53 + 2 * KRAS - 1.3 * PTEN"</code>).</dd>


<dt>data_type</dt>
<dd>data type. Can be one of "mRNA", "transcript", "protein",
"mutation", "cnv", "methylation", "miRNA".</dd>


<dt>out_dir</dt>
<dd>path to save analysis result and report, default is '.'</dd>


<dt>out_report</dt>
<dd>logical value wheather to generate html report</dd>

</dl>

mol_quick_analysis: Quick molecule analysis and report generation

Description

Usage

Value

Arguments