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

Description Usage Arguments Value Examples

View source: R/rampFastQueryTab3.R

Description

Filter pathways by p-value cutoff for display and clustering

Usage

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FilterFishersResults(fishers_df, p_holmadj_cutoff = NULL,
  p_fdradj_cutoff = NULL)

Arguments

fishers_df

The data frame generated by runFisherTest

p_holmadj_cutoff

return pathways where Holm adjusted pvalues are < p_holmadj_cutoff

p_fdradj_cutoff

return pathways where FDR adjusted pvalues are < p_fdradj_cutoff

Value

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

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)
filtered.fisher.results <- FilterFishersResults(fisher.results,p_holmadj_cutoff=0.05)

## End(Not run)

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