nw_pathway_activity

Source: R/nw_pathway_activity.R

This function returns node and edge tables that can be used to generate a network using the network visualization tool. It computes flux changes in the lipid reaction network, facilitating the identification of active or suppressed pathways.

nw_pathway_activity(deSp_se, organism = c("human", "mouse"))

Arguments

deSp_se

A SummarizedExperiment object with results computed by deSp_twoGroup.

organism

Character. The species to which the genes will be matched. Allowed species are "human" and "mouse". Default is 'human'.

Value

Return a list of 4 tables.

  1. table_edge: a table of network edges.

  2. table_node; a table of network nodes.

  3. table_pathway_score: a table of pathway score

  4. table_zScore: a table of z score.

Examples

data("de_data_twoGroup")
processed_se <- data_process(
    se=de_data_twoGroup, exclude_missing=TRUE, exclude_missing_pct=70,
    replace_na_method='min', replace_na_method_ref=0.5,
    normalization='Percentage')
deSp_se <- deSp_twoGroup(
    processed_se, ref_group='ctrl', test='t-test',
    significant='pval', p_cutoff=0.05, FC_cutoff=1, transform='log10')
network_table <- nw_pathway_activity(deSp_se, organism='mouse')