categorize_sex_sc

Identifies male-specific, female-specific, sex-dimorphic, and sex-neutral DEGs from differential expression results.

Tools to analyze sex differences in omics data for complex diseases. It includes functions for differential expression analysis using the 'limma' method <doi:10.1093/nar/gkv007>, interaction testing between sex and disease, pathway enrichment with 'clusterProfiler' <doi:10.1089/omi.2011.0118>, and gene regulatory network (GRN) construction and analysis using 'igraph'. The package enables a reproducible workflow from raw data processing to biological interpretation.

Enrico Glaab

XYomics

Analysis of Sex Differences in Omics Data for Complex Diseases

Sophie Le Bars

Mohamed Soudy

Murodzhon Akhmedov

categorize_sex_sc function

<dl><dt>male_degs</dt>
<dd>Data frame containing male differential expression results from one specific cell-type or bulk dataset.</dd>
<dt>female_degs</dt>
<dd>Data frame containing female differential expression results from one specific cell-type or bulk dataset.</dd>
<dt>target_fdr</dt>
<dd>Numeric. FDR threshold for significance.</dd>
<dt>exclude_pval</dt>
<dd>Numeric. P-value threshold for excluding genes in opposite sex.</dd>
<dt>min_abs_logfc</dt>
<dd>Numeric. Minimum absolute log2 fold change threshold.</dd></dl>

Arguments

Compute sex-specific differentially expressed genes (DEGs) per category — categorize_sex_sc

<dl>

<dt>male_degs</dt>
<dd>Data frame containing male differential expression results from one specific cell-type or bulk dataset.</dd>


<dt>female_degs</dt>
<dd>Data frame containing female differential expression results from one specific cell-type or bulk dataset.</dd>


<dt>target_fdr</dt>
<dd>Numeric. FDR threshold for significance.</dd>


<dt>exclude_pval</dt>
<dd>Numeric. P-value threshold for excluding genes in opposite sex.</dd>


<dt>min_abs_logfc</dt>
<dd>Numeric. Minimum absolute log2 fold change threshold.</dd>

</dl>

categorize_sex_sc: Compute sex-specific differentially expressed genes (DEGs) per category

Description

Usage

Value

Arguments