mgi_from_sif: Create a Pathways object from SIF files

In hipathia: HiPathia: High-throughput Pathway Analysis

Description

Creates a Pathways object from the information of a pathway stored in a SIF file with some attributes. This pathways object can be used by function hipathia to analyze data.

Usage

mgi_from_sif(sif.folder, spe, entrez_symbol = NULL, dbannot = NULL)

Arguments

sif.folder	Path to the folder in which SIF and ATT files are stored.
spe	Species
entrez_symbol	Relation between Entrez (NCBI) genes and gene symbols. Data.frame with 2 columns: First column is the EntrezGene ID, second column is the gene Symbol. The genes in the nodes of the pathways should be defined by Entrez IDs in the SIF and ATT files of the pathways. In order to be more readable, gene names are used when plotting the pathways.
dbannot	Functional annotation of the genes in the pathways to create function nodes.

Value

A pathways object with the same structure of that returned by function load_pathways.

hipathia documentation built on Nov. 8, 2020, 7:52 p.m.