selectPathways

This function randomly selects a specified number of pathways from a given list, ensuring that each selected pathway name does not exceed a specified number of words. It filters out pathways with names longer than the specified word limit before making the selection.

A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10.1186/s13059-022-02648-4>), providing flexible and robust approaches to RNA-Seq data analysis. For more information, refer to the package vignettes and related publications.

Dongyue Yu

TransProR

Analysis and Visualization of Multi-Omics Data

selectPathways function

<dl><dt>pathways</dt>
<dd>Character vector of pathways.</dd>
<dt>max_words</dt>
<dd>Integer, maximum number of words allowed in the pathway name.</dd>
<dt>num_select</dt>
<dd>Integer, number of pathways to randomly select.</dd></dl>

Arguments

Randomly Select Pathways with Limited Word Count — selectPathways

<dl>

<dt>pathways</dt>
<dd>Character vector of pathways.</dd>


<dt>max_words</dt>
<dd>Integer, maximum number of words allowed in the pathway name.</dd>


<dt>num_select</dt>
<dd>Integer, number of pathways to randomly select.</dd>

</dl>

selectPathways: Randomly Select Pathways with Limited Word Count

Description

Usage

Value

Arguments

Examples