FilterFishersResults: Filter pathways by p-value cutoff for display and clustering

View source: R/rampQueryHelper.R

FilterFishersResultsR Documentation

Filter pathways by p-value cutoff for display and clustering

Description

Filter pathways by p-value cutoff for display and clustering

Usage

FilterFishersResults(fishers_df, pval_type = "fdr", pval_cutoff = 0.1)

Arguments

fishers_df

The data frame generated by runFisherTest

pval_type

Specifies which p-value to use as the filter threshold. Permitted values are 'pval' and 'fdr' for chemical class and pathway enrichment. Pathway enrichment also includes an optional 'holm' value for holm p-value corrections. Default is 'fdr'.

pval_cutoff

return pathways where pval_type p-values are < pval_cutoff

Value

list:[[1]]Dataframe with pathway enrichment results, only significant pathways [[2]]analyte type

Examples

## Not run: 
pkg.globals <- setConnectionToRaMP(
  dbname = "ramp2", username = "root",
  conpass = "", host = "localhost"
)
analyteList <- c("MDM2", "TP53", "glutamate", "creatinine"),

fisher.results <- runCombinedFisherTest(analytes = analytesList, NamesOrIds = 'names')
filtered.fisher.results <- FilterFishersResults(fisher.results, pval_type='fdr', pval_cutoff = 0.10)

## End(Not run)

ncats/RaMP-DB documentation built on May 6, 2022, 1:35 a.m.