Skip to contents

Retrieve the regulatory status of deregulated genes

Source: R/getregs.R
getregs.Rd

This function retrieves information on the regulatory status of genes using the files downloaded with the dl_regulation_data() function.

Usage

getregs(getids_data, regulator_file, coregulator_file)

Arguments

getids_data

A dataframe of type t that typically corresponds to the output of the getids() function. This input holds at least one column named "gene_id" holding gene identifiers for the deregulated genes. It should be a subset of the output of the getids() function with only the significantly deregulated transcripts as rows and transcript/gene identifiers as columns.

regulator_file

The previously downloaded .txt Transcription Factor file from the AnimalTFDB4 database (https://guolab.wchscu.cn/AnimalTFDB4/#/).

coregulator_file

The previously downloaded .txt Transcription Co-Factor file from the AnimalTFDB4 database (https://guolab.wchscu.cn/AnimalTFDB4/#/).

Value

A dataframe of type t similar to the getids_data input with an added column indicating the (co-)regulator status of each transcript's deregulated gene.