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

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

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

Description

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

Usage

runEnrichPathways(
  analytes,
  namesOrIds = "ids",
  totalGenes = 20000,
  minAnalyte = 2,
  alternative = "less",
  minPathwaySize = 5,
  maxPathwaySize = 150,
  includeRaMPids = FALSE,
  backgroundType = "database",
  background = "database",
  pathwayDefinitions = "RaMP",
  includeSmpdb = FALSE,
  db = RaMP()
)

Arguments

analytes	a vector of analytes (genes or metabolites) that need to be searched
namesOrIds	whether input is "names" or "ids" (default is "ids", must be the same for analytes and background)
totalGenes	number of genes analyzed in the experiment (e.g. background) (default is 20000, with assumption that analyteType is "genes")
minAnalyte	if the number of analytes (gene or metabolite) in a pathway is < minAnalyte, do not report
alternative	alternative hypothesis test passed on to fisher.test(). Options are two.sided, greater, or less (default is "less")
minPathwaySize	the minimum number of pathway members (genes and metabolites) to include the pathway in the output (default = 5)
maxPathwaySize	the maximum number of pathway memnbers (genes and metaboltes) to include the pathway in the output (default = 150)
includeRaMPids	include internal RaMP identifiers (default is "FALSE")
backgroundType	type of background that is input by the user. Opions are "database" if user wants all analytes from the RaMP database to be used as background; "file", if user wnats to input a file path with a list of background analytes; "list", if user wants to input a vector of analyte IDs; "biospecimen", if user wants to specify a biospecimen type (e.g. blood, adipose tissue, etc.) and have those biospecimen-specific analytes used. For genes, only the "database" option is used.
background	background to be used for Fisher's tests. If parameter 'backgroundType="database"', this parameter is ignored (default="database"); if parameter 'backgroundType= "file"', then 'background' should be a file name (with directory); if 'backgroundType="list"', then 'background' should be a vector of RaMP IDs; if 'backgroud_type="biospecimen"' then users should specify one of the following: "Blood", "Adipose tissue", "Heart", "Urine", "Brain", "Liver", "Kidney", "Saliva", and "Feces"
pathwayDefinitions	If "RaMP" (default), use pathway definitions within RaMP-DB. Else, supply path to gmx file containing custom pathway definitions. GMX files are a tab-separated format that contain one analyte set per column, with the name of the set in the first row, and constituent analytes in subsequent rows. Please supply a .xls or .xlsx file. If supplying pathway definitions for genes and metabolites, ensure that metabolite definitions are on tab 1, and gene definitions are on tab2.
includeSmpdb	Include pathways from smpdb/hmdb in analysis. Excluded by default since definitions are highly redundant
db	a RaMP databse object

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]] analyteType, a string specifying the type of analyte input into the function ("genes", "metabolites", or "both") [[3]] result_type, a string specifying pathway enrichment was performed

Examples

## Not run: 
fisher.results <- runEnrichPathways(analytes = c("ensembl:ENSG00000135679", "hmdb:HMDB0000064",
"hmdb:HMDB0000148", "ensembl:ENSG00000141510"))

fisher.results <- runEnrichPathways(analytes = analyte.list, namesOrIds = "ids")

## End(Not run)

ncats/RaMP-DB documentation built on June 10, 2025, 10:50 a.m.