func2vis (version 1.0-3)

clean_pathways: Clean Enriched Pathways

Description

Clean set of enriched pathways obtained from 'ConsensusPathDB' for gene set overexpression analysis. We also append two columns indicating the number of up-regulated and number of down-regulated genes based on fold change information available in data frame case_vs_ctrl. We cluster pathways based on similarity of gene set using igraph's walktrap clustering algorithm. Within each cluster, pathways are ordered by most to least significant pathway in terms of p-values.

Usage

clean_pathways(df_case_vs_ctrl, df_pathway)

Value

Returns clean enriched pathways data frame. The data frame has an additional column clusters highlighting the cluster to which each enriched pathway belongs.

Arguments

df_case_vs_ctrl

Data frame which has at least 2 columns: <gene,fc>. Here gene represents the set of genes which are differentially expressed between case and control. Here fc represents the fold-change value for each gene.

df_pathway

The tab-separated data frame with the pathways information obtained after performing gene set overexpression analysis using 'ConsensusPathDB'.

Author

Raghvendra Mall

See Also

clean_go_terms, clean_pc

Examples

data("t.tests.treatment.sign")
data("enriched_pathways")
revised_pathway <- clean_pathways(df_case_vs_ctrl=t.tests.treatment.sign,
                                  df_pathway = enriched_pathways)
print(head(revised_pathway))