get_motif_info: Generate a Top Motif List Adjacent to Input Genes Based on...

In chenyenchung/genofeatutil: Utilities for genomic feature manipulation

Description

get_motif_info() reads a motif scoring table and motif name table from RcisTarget, and then filter it according to the set threshold on score or the number of candidates to keep. it returns a list, in which the names of the items are the name of the target gene, and each item is a character vector of transcription factors.

Usage

get_motif_info(score_path, motif_path, number = NULL, threshold = NULL,
  genes.use = NULL, db)

Arguments

score_path	a character string of the path to the scoring database from SCENIC / RcisTarget
motif_path	a character string of the path to the motif database from SCENIC / RcisTarget
number	a number of motifs with the highest score to leave from the motif list
threshold	a number of score threshold to filter the motifs
genes.use	a character vector to leave only the genes of interest ( Usually the targets) in the output motif list
db	a list from make_database()

Value

a list of genes and related transcription factors based on motif info

chenyenchung/genofeatutil documentation built on May 15, 2019, 10:38 p.m.