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

Description Usage Arguments Value

View source: R/rampFastQueryTab3.R

Description

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

Usage

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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


ncats/RaMP-DB documentation built on Nov. 21, 2020, 7:41 p.m.