mine_step2 {cageminer}R Documentation

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.

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(pepper_se, gcn = gcn, guides = guides$Gene,
                    candidates = rownames(pepper_se))

[Package cageminer version 0.99.7 Index]