plot_polyviolinr: Plots a violin plot showing the gene-score distribution of...

In ACAD-UofA/PolyLinkR: Polygenic Pathway Enrichment Accounting for Genetic Linkage

Description

Plots a violin plot showing the gene-score distribution of the enriched gene sets/pathways above a give q-value and/or p-value cutoff(s)

Usage

plot_polyviolinr(
  polylinkr.out,
  set.info,
  obj.info,
  set.obj,
  p.cutoff = 0,
  q.cutoff = 0
)

Arguments

polylinkr.out	data.table: output of polylinkr function
set.info	data.frame: four required fields; gene IDs, associated scores, chromosome, and start position
obj.info	data.frame: two required fields; genomic regions and associated scores
set.obj	data.frame: two required fields; genomic regions and associated scores
p.cutoff	float: desired p-value enrichement cutoff
q.cutoff	float: desired q-value enrichement cutoff

Value

Returns a ggplot object.

See Also

polylinkr, PolyLinkR_SetInfo, PolyLinkR_SetObj, Anatolia_EF_CLR

Examples

output = (obj.info = Anatolia_EF_CLR, set.info = PolyLinkR_SetInfo, 
          set.obj = PolyLinkR_SetObj, n.cores = 8, emp.nruns = 1000, NN = 10000)
p = plot_polyviolinr(polylinkr.out =  output, obj.info = Anatolia_EF_CLR, 
                     set.info = PolyLinkR_SetInfo, set.obj = PolyLinkR_SetObj, p.cutoff = 0.001)

ACAD-UofA/PolyLinkR documentation built on Dec. 31, 2020, 9:44 a.m.