topAnatEnrichment-methods: Enrichment of a user's input (genes) in anatomical terms...

In aGutierrezSacristan/psygenet2r: psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

Enrichment of a user's input (genes) in anatomical terms (TopAnat).

Description

Test the enrichment of a given gene list on Psychiatric Disorders from PsyGeNET.

Usage

topAnatEnrichment(gene, datatype = c("rna_seq", "affymetrix", "est",
  "in_situ"), statistic = "fisher", cutOff = 1, verbose = FALSE,
  warnings = FALSE)

Arguments

gene	Name or vector of names (that can be both code or uml) to specific genes from PsyGeNET.
datatype	It can take the values 'rna_seq', 'affymetrix', "est" or "in situ". Default c("rna_seq","affymetrix","est","in_situ").
statistic	By default it is "fisher". But it can be changed to "ks", "t", "globaltest", "sum" or "ks.ties". All from runTest.
cutOff	Default 1.
verbose	By default FALSE. Change it to TRUE to get a on-time log from the function.
warnings	By default TRUE. Change it to FALSE to not see the warnings.

Value

A data.frame with the enrichment results

Examples

## Not run: 
topAnatEnrichment(gene=c("ADCY2", "AKAP13", "ANK3"))

## End(Not run)

aGutierrezSacristan/psygenet2r documentation built on Jan. 18, 2024, 4:06 a.m.