runCombinedFisherTest: Do fisher test for only one pathway from search result...
In Mathelab/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

Description Usage Arguments Value Examples

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

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runCombinedFisherTest(pathwaydf, total_metabolites = NULL,
  total_genes = 20000, min_analyte = 2, conpass = NULL,
  dbname = "ramp", username = "root", host = "localhost")

`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")

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")

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

## End(Not run)