find_bifan: Find bifan motifs

In almeidasilvaf/magrene: Motif Analysis In Gene Regulatory Networks

Find bifan motifs

Description

Find bifan motifs

Usage

find_bifan(
  edgelist = NULL,
  paralogs = NULL,
  lambda_vec = NULL,
  count_only = FALSE
)

Arguments

edgelist	A 2-column data frame with regulators in column 1 and targets in column 2. It can be ignored if you give lambda motifs to parameter lambda_vec (recommended).
paralogs	A 2-column data frame with gene IDs for each paralog in the paralog pair.
lambda_vec	A character of lambda motifs as returned by find_lambda(). If this is NULL, this function will find lambda motifs from edgelist and paralogs first. Passing previously identified lambda motifs will make this function much faster.
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 bifan motifs represented in the format regulator1, regulator2->target1, target2.

Examples

data(gma_grn)
data(gma_paralogs)
edgelist <- gma_grn[1:50000, 1:2]
paralogs <- gma_paralogs[gma_paralogs$type == "WGD", 1:2]
paralogs <- rbind(
paralogs,
data.frame(duplicate1 = "Glyma.01G177200", 
           duplicate2 = "Glyma.08G116700")
)
lambda_vec <- find_lambda(edgelist, paralogs)
bifan <- find_bifan(paralogs = paralogs, lambda_vec = lambda_vec)

almeidasilvaf/magrene documentation built on March 16, 2023, 4:29 a.m.