Step 2: Get candidates in modules enriched in guide genes

Usage

mine_step2(exp, gcn, guides, candidates, ...)

Arguments

exp: Expression data frame with genes in row names and samples in column names or a SummarizedExperiment object.
gcn: Gene coexpression network returned by BioNERO::exp2gcn().
guides: Guide genes as a character vector or as a data frame with genes in the first column and gene annotation class in the second column.
candidates: Character vector of all candidates genes to be inspected.
...: Additional arguments to BioNERO::module_enrichment

Value

A list of 2 elements:

candidates: Character vector of candidates after step 2
enrichment: Data frame of results for enrichment analysis

Examples

data(pepper_se)
data(guides)
data(gcn)
set.seed(1)
mine2 <- mine_step2(
    exp = pepper_se,
    gcn = gcn,
    guides = guides$Gene,
    candidates = rownames(pepper_se)
)
#> Enrichment analysis for module cyan...