nw_lipid_reaction

Source: R/nw_lipid_reaction.R

This function returns node and edge tables that can be used to generate a network using the network visualization tool. It is designed to graphically represent significant lipid classes and species within lipid biosynthesis pathways.

nw_lipid_reaction(
  deSp_se,
  organism = c("human", "mouse"),
  show_sp = c("all", "sigClass", "none"),
  show_all_reactions = FALSE,
  sp_significant = c("pval", "padj"),
  sp_p_cutoff = 0.05,
  sp_FC_cutoff = 1,
  class_significant = c("pval", "padj"),
  class_p_cutoff = 0.05,
  class_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'.

show_sp

Character. Determine how lipid species around the lipid class will be displayed. Must be one of "all", "sigClass", and "none". Select "all" to show all species, "sigClass" to show species in significant lipid classes, and "none" to not show any species. Default is 'sigClass'.

show_all_reactions

Logical. If show_all_reactions=TURE, all the reactions will be showed. Default is FALSE.

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.

class_significant

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

class_p_cutoff

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

class_FC_cutoff

Numeric. Significance of the fold-change of lipid class. 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_lipid_reaction(
    deSp_se, organism='mouse', show_sp='sigClass', show_all_reactions=FALSE,
    sp_significant='pval', sp_p_cutoff=0.05, sp_FC_cutoff=1,
    class_significant='pval', class_p_cutoff=0.05, class_FC_cutoff=1)