nw_gatom

This function returns node and edge tables that can be used to generate a network using the network visualization tool. It isolates significant subnetworks within a constructed metabolite-level network.

nw_gatom(
  deSp_se,
  organism = c("human", "mouse"),
  n_lipid = 50,
  sp_significant = c("pval", "padj"),
  sp_p_cutoff = 0.05,
  sp_FC_cutoff = 1
)

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'.

n_lipid

Numeric. The number of lipids to be scored positively determines the size of the resulting module. The higher the number, the larger the module. Default is 50.

sp_significant

Character. The p-value to be used for the statistically significant of lipid species. Must be one of "pval" or "padj". Default is 'pval'.

sp_p_cutoff

Numeric. Significant level of lipid species. Default is 0.05.

sp_FC_cutoff

Numeric. Significance of the fold-change of lipid species. Default is 1.

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_reaction: a table of reactions.

4. table_stat: a table of statistical results.

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_gatom(
    deSp_se, organism='mouse', n_lipid=50, sp_significant='pval',
    sp_p_cutoff=0.05, sp_FC_cutoff=1)
#> Registered S3 method overwritten by 'GGally':
#>   method from   
#>   +.gg   ggplot2
#> Found DE table for metabolites with Species IDs
#> Warning: One or both parameters are on the limit of the defined parameter space
#> Metabolite p-value threshold: 1.000000
#> Metabolite BU alpha: 0.043884
#> FDR for metabolites: 0.043894