mine_step2 {cageminer} | R Documentation |
Step 2: Get candidates in modules enriched in guide genes
mine_step2(exp, gcn, guides, candidates)
exp |
Expression data frame with genes in row names and samples in column names or a SummarizedExperiment object. |
gcn |
Gene coexpression network returned by |
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. |
A list of 2 elements:
Character vector of candidates after step 2
Data frame of results for enrichment analysis
data(pepper_se) data(guides) data(gcn) set.seed(1) mine2 <- mine_step2(pepper_se, gcn = gcn, guides = guides$Gene, candidates = rownames(pepper_se))