gosty: Functional enrichment of a gene list with gprofiler2

In ATpoint/diffanalyseR: Wrapper functions for common tasks related to analysis of NGS counts data

Description

Function minimally expects a vector of genes which will be used for functional enrichment analysis with GOST (g:profiler2). Optionally (and recommended) is a list of background genes. One can specify organism and databases to scan against. See '?gost', this here is just a simple wrapper to bring output into a more parsable format.

Usage

gosty(
  InputGenes,
  BackgroundGenes = NULL,
  Species = "mmusculus",
  Sources = c("KEGG", "REAC"),
  FDR.threshold = 0.05,
  ...
)

Arguments

InputGenes	vector with gene names (HGNC/MGI/Ensembl)
BackgroundGenes	vector with gene names (HGNC/MGI/Ensembl)
Species	mmusculus/hsapiens etc...
Sources	the databases to use, default is c("KEGG", "REAC")
FDR.threshold	FDR threshold for significance, if NULL return all hits
...	further arguments for gprofiler2::gost()

Author(s)

Alexander Toenges

Examples

gosty(InputGenes = c("Ets1", "Cebpa", "Cd14", "Gapdh", "Spi1", "Cebpe"))

ATpoint/diffanalyseR documentation built on Oct. 8, 2021, 10:11 p.m.