Description Usage Arguments Value
Do fisher test for only one pathway from search result clicked on highchart
1 2 3 | runFisherTest(pathwaydf, total_metabolites = NULL, total_genes = 20000,
analyte_type = "metabolites", conpass = NULL, dbname = "ramp",
username = "root")
|
pathwaydf |
a data frame resulting from rampFastPathFromMeta |
total_metabolites |
number of metabolites analyzed in the experiment (e.g. background) (default is total number of metabolites that map to a pathway in RaMP, with 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") |
a dataframe with pathway enrichment (based on Fisher's test) results
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