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

topAnatEnrichmentR Documentation

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.