mine_step2: Step 2: Get candidates in modules enriched in guide genes

In almeidasilvaf/cageminer: Candidate Gene Miner

Step 2: Get candidates in modules enriched in guide genes

Description

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)
)

almeidasilvaf/cageminer documentation built on Sept. 9, 2023, 5:18 p.m.