PAGnetMRA: PAGnet: Pseudomonas aeruginosa genomic integrated regulatory...

In CityUHK-CompBio/PAGnet: PAGnet: Pseudomonas aeruginosa genomic integrated regulatory network.

Description

This function perform master regulator analysis (MRA) over a list of regulons from the default PAGnet or user uploaded regulator network for identification of key transcription factors mediating a biological process or pathway.

Usage

  pagnet.mra(rnet=pagnet, tflist=tf, signature=qs, pValueCutoff=0.05)

Arguments

rnet	a regulatory network in Pseudomonas aeruginosa genomic netork.The user can choose to use the default PAVIRnet or to upload their own regulatory network in a predefined format
tflist	a list of transcription factor in regulatory network.
signature	interested gene sets.
pValueCutoff	a single numeric value specifying the cutoff for p-values considered significant.

Examples

  data(PAGnet)

  #Use PAGnet as regulatory network
  #Select quorum sensing (QS) related genes as signatures
  #run MRA

  MRA_results <- pagnet.mra(rnet=pagnet,tflist=tf,signature = qs, pValueCutoff = 0.05)

  #Having completed master regulator analysis, a table will be returned
  head(MRA_results)

CityUHK-CompBio/PAGnet documentation built on May 3, 2019, 3:19 p.m.