parseStringKB: parseStringKB

In umbibio/CIE-R-Package: Causal Inference and Directional Enrichment Methods on Biological Networks

parseStringKB

Description

Process STRINGdb data into a format usable by this enrichment pipeline. Assumes that if a protein targets a protein it also targets the gene.

Usage

parseTRED(in.file)

Arguments

ents.file	A tab separated file containing the entries of STRINGdb
rels.file	A tab separated file describing the interactions between the entries of STRINGdb
verbose	A boolean value, indicating whether the output should include verbose messaging. Defaults to FALSE.

Value

A list of two dataframes, ents and rels. The ents dataframe is all the entries from the selected database. The rels table describes the relations between the entries

Examples

entsRels <- parseStringKB("string.ents", "string.rels")
ents <- entsRels$ents
rels <- entsRels$rels

umbibio/CIE-R-Package documentation built on Sept. 26, 2023, 3:37 a.m.