Classify genes into unique modes of duplication

Usage

classify_genes(gene_pairs_list = NULL)

Arguments

gene_pairs_list: List of classified gene pairs as returned by classify_gene_pairs().

Value

A list of 2-column data frames with variables gene and type representing gene ID and duplication type, respectively.

Details

If a gene is present in pairs with different duplication modes, the gene is classified into a unique mode of duplication following the order of priority indicated in the levels of the factor type.

For scheme "binary", the order is SD > SSD. For scheme "standard", the order is SD > TD > PD > DD. For scheme "extended", the order is SD > TD > PD > TRD > DD. For scheme "full", the order is SD > TD > PD > rTRD > dTRD > DD.

Examples

data(fungi_kaks)
scerevisiae_kaks <- fungi_kaks$saccharomyces_cerevisiae

cols <- c("dup1", "dup2", "type")
gene_pairs_list <- list(Scerevisiae = scerevisiae_kaks[, cols])

class_genes <- classify_genes(gene_pairs_list)