get_candidate_gene: —————— Get the candidate gene of a locus using...

In matthiasheinig/QTLnetwork: Basic package to apply random walks for QTL candidate gene priorization

Description

Applys the random walk approach to get the most likely SNP gene from the list of provided SNP genes

Usage

get_candidate_gene(snp_id, snp_genes, trans_cpgs, ppi_graph,
  tfbs_annotation, gene_only = FALSE)

Arguments

snp_id	Character id of the SNP in the locus
snp_genes	Character vector of the genes encoded near the SNP
trans_cpgs	Character vector of the trans CpGs associated to the SNP
ppi_graph	graphNEL object containing the PPIs (e.g. from STRING)
tfbs_annotation	Logical indicator matrix with trans entities in the rows and transcription factors as columns (bincinding site information of transcription factors at trans entities)
gene_only	Logical whether to return only the identified candidate gene or also the rest of the random walk results (default: FALSE)

Value

The candidate gene as determined by the random walk analysis

Author(s)

Johann Hawe <[e-mail]>

#'@examples ## Not run: data(ppi_string) data(test_data) data(tfbs_annotation) candidate_gene <- get_candidate_gene(snp_id, snp_genes, trans_cpgs, ppi_string, tfbs_annotation, gene_only = TRUE) print(candidate_gene) ## End(Not run) —————————————————————————–

matthiasheinig/QTLnetwork documentation built on June 29, 2021, 10:11 p.m.