quackPrediction: Quack prediction function

In lagelab/quack: Pathway analysis by learning connectivity patterns in known pathways and making gene prediction

Description

Using the trained model from user uploaded network, using seed genes, predict genes that should be in a network.

Usage

quackPrediction(usr_network_name, usr_seed_file, trained_network_file,
  quack_gene_model, usr_output_loc, usr_pathway_file)

Arguments

usr_network_name	Characters of user's network name, used in make graphs and train model functions.
usr_seed_file	Characters of path and name of user's seed file containing list of genes.
trained_network_file	Characters of path and name to network file from make graphs function.
quack_gene_model	Characters of path and name to quack gene model created from train model function.
usr_output_loc	Characters of location to save output file.
usr_pathway_file	Characters of name of pathway files, which can be found in data/ or user uploaded.

Value

text file

Examples

quackPrediction("InWeb3", "data/SandersGenes.txt", "data/InWeb3.RData", "QuackGeneModel_Quackv1.3-InWeb3-General853StringentPathways.RData", "data/", "data/stringent853Pathways.RData")

lagelab/quack documentation built on May 25, 2019, 9:30 p.m.