topAnatEnrichment {psygenet2r} | R 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)

[Package psygenet2r version 1.22.5 Index]