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

Description Usage Arguments Value Examples

View source: R/rampFastQueryTab3.R

Description

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

Usage

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runCombinedFisherTest(pathwaydf, total_metabolites = NULL,
  total_genes = 20000, min_analyte = 2, 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")

min_analyte

if the number of analytes (gene or metabolite) in a pathway is < min_analyte, do not report

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 list containing two entries: [[1]] fishresults, a dataframe containing pathways with Fisher's p values (raw and with FDR and Holm adjustment), number of user analytes in pathway, total number of analytes in pathway, and pathway source ID/database. [[2]] analyte_type, a string specifying the type of analyte input into the function ("genes", "metabolites", or "both")

Examples

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## Not run: 
pathwaydf<-getPathwayFromAnalyte(c("MDM2","TP53","glutamate","creatinine"),
                NameOrIds="names", conpass=conpass)
fisher.results <- runCombinedFisherTest(pathwaydf=pathwaydf,conpass=conpass)

## End(Not run)

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