subset_by_size: Filter of ontology enrichment results by size

In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

Description

This utility works to filter results of enrich* test from cluterProfiler-package, DOSE-package or ReactomePA-package

Usage

subset_by_size(
  x,
  minObsSize = 0,
  maxObsSize = Inf,
  minSetSize = 0,
  maxSetSize = Inf
)

Arguments

x	is an enrichResults instance
minObsSize	mininum number of genes must be observed per set
maxObsSize	maxinum number of genes must be in the set
minSetSize	mininum number of genes must be in the set

Value

filtered enrichResults isntance

Examples

library(clusterProfiler)
data(gcSample)
x <- enrichGO(gcSample[[6]], 
              universe = unique(unlist((gcSample))),
              ont = "CC", 
              pvalueCutoff = 1, 
              qvalueCutoff = 1, 
              minGSSize = 0)
res <- summary(x)
res$geneID <- NULL
rownames(res) <- NULL
head(res)
cnetplot(x)

# E.g. the "cell", "cell part" & "cellular_component" seem too generic
x <- subset_by_size(x, maxObsSize=50)
res <- summary(x)
res$geneID <- NULL
rownames(res) <- NULL
# Now they are gone
head(res)
cnetplot(x)

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.