func2vis (version 1.0-3)

clean_pc: Clean Enriched Protein Complexes

Description

Clean set of enriched protein complexes 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.

Usage

clean_pc(df_case_vs_ctrl,df_pc)

Value

Returns clean enriched protein complexes data frame.

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_pc

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

Author

Raghvendra Mall

See Also

See Also as clean_go_terms, plot_go_terms

Examples

data("t.tests.treatment.sign")
data("enriched_pc")
revised_pc <- clean_pc(df_case_vs_ctrl=t.tests.treatment.sign,
                                  df_pc = enriched_pc)
print(head(revised_pc))