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Find V motifs

Source: R/motif_identification.R
find_v.Rd

Find V motifs

Usage

find_v(edgelist = NULL, paralogs = NULL, count_only = FALSE)

Arguments

edgelist

A 2-column data frame with regulators in column 1 and targets in column 2.

paralogs

A 2-column data frame with gene IDs for each paralog in the paralog pair.

count_only

Logical indicating whether the function should return only motif counts as a numeric scalar. If FALSE, it will return a character vector of motifs. Default: FALSE.

Value

A character vector with V motifs represented in the format regulator1->target<-regulator2.

Examples

data(gma_grn)
data(gma_paralogs)
edgelist <- gma_grn[2000:4000, 1:2] # reducing for test purposes
paralogs <- gma_paralogs[gma_paralogs$type == "WGD", 1:2]
motifs <- find_v(edgelist, paralogs)