prepare_rnk

Prepare .rnk file for GSEA preranked analysis

Streamlined workflow from deconvolution of bulk RNA-seq data to downstream differential expression and gene-set enrichment analysis. Provide various visualization functions.

Yuanhang Liu

SCdeconR

Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq
Data as Reference

prepare_rnk function

<dl><dt>teststats</dt>
<dd>a data.frame containing differential expression results with five columns: "Gene name", "log2 fold change", "log2 average expression",
"p value", "adjusted p value". The second element of the output from function <code>run_de</code>.</dd>
<dt>outputfile</dt>
<dd>full path including file name to .rnk file.</dd>
<dt>replace</dt>
<dd>a logical value indicating whether to replace the output file if it already exists. Default to FALSE.</dd></dl>

Arguments

Prepare .rnk file for GSEA preranked analysis — prepare_rnk

<dl>

<dt>teststats</dt>
<dd>a data.frame containing differential expression results with five columns: "Gene name", "log2 fold change", "log2 average expression",
"p value", "adjusted p value". The second element of the output from function <code>run_de</code>.</dd>


<dt>outputfile</dt>
<dd>full path including file name to .rnk file.</dd>


<dt>replace</dt>
<dd>a logical value indicating whether to replace the output file if it already exists. Default to FALSE.</dd>

</dl>

prepare_rnk: Prepare .rnk file for GSEA preranked analysis

Description

Usage

Value

Arguments