get.TF_SIG.list: Get Transcription Factor (TF) and Signaling Factor (SIG) List

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Get Transcription Factor (TF) and Signaling Factor (SIG) List

Description

get.TF_SIG.list is a function converts gene ID into the corresponding TF/SIG list, with selected gene/transcript type.

Usage

get.TF_SIG.list(
  use_genes = NULL,
  use_gene_type = "external_gene_name",
  ignore_version = FALSE,
  dataset = NULL
)

Arguments

use_genes	a vector of characters, genes will be used in the network construction. If NULL, no filter will be performed to the TF/SIG list. Default is NULL.
use_gene_type	character, the attribute name inherited from the biomaRt package. Some options are, "ensembl_gene_id", "ensembl_gene_id_version", "ensembl_transcript_id", "ensembl_transcript_id_version" and "refseq_mrna". All options can be accessed by calling biomaRt::useMart (e.g. mart <- biomaRt::useMart('ensembl',db_info[1]); biomaRt::listAttributes(mart)$name). The type must match the gene type from the input use_genes. Default is "external_gene_name".
ignore_version	logical, if TRUE, the version "ensembl_gene_id_version" or "ensembl_transcript_id_version" will be ignored. Default is FALSE.
dataset	character, the dataset used for ID conversion (e.g. "hsapiens_gene_ensembl"). If NULL, use db_info[1] from db.preload. Default is NULL.

Value

Return a list containing two elements. tf is the TF list, sig is the SIG list.

Examples

db.preload(use_level='transcript',use_spe='human',update=FALSE)
use_genes <- c("ENST00000210187","ENST00000216083","ENST00000216127",
             "ENST00000216416","ENST00000217233","ENST00000221418",
             "ENST00000504956","ENST00000507468")
res_list  <- get.TF_SIG.list(use_gene_type = 'ensembl_transcript_id',
                               use_genes=use_genes,
                               dataset='hsapiens_gene_ensembl')
print(res_list)

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jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.