clean_pathways {func2vis}

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)

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'.

Value

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

Note

[e-mail]

Author(s)

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))