runFisherTest: Do fisher test for only one pathway from search result...

In Mathelab/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

Description

Do fisher test for only one pathway from search result clicked on highchart

Usage

runFisherTest(pathwaydf, total_metabolites = NULL, total_genes = 20000,
  analyte_type = "metabolites", conpass = NULL, dbname = "ramp",
  username = "root", host = "localhost")

Arguments

pathwaydf	a data frame resulting from getPathwayFromAnalyte
total_metabolites	number of metabolites analyzed in the experiment (e.g. background) (default is 1000; set to 'NULL' to retrieve total number of metabolites that map to any pathway in RaMP). Assumption that analyte_type is "metabolite")
total_genes	number of genes analyzed in the experiment (e.g. background) (default is 20000, with assumption that analyte_type is "genes")
analyte_type	"metabolites" or "genes" (default is "metabolites")
conpass	password for database access (string)
dbname	name of the mysql database (default is "ramp")
username	username for database access (default is "root")
host	host name for database access (default is "localhost")

Value

a dataframe with columns containing pathway ID, fisher's p value, user analytes in pathway, and total analytes in pathway

Mathelab/RaMP-DB documentation built on April 24, 2021, 3:11 p.m.