sigidentEnrichment: Perform Enrichtment Analysis in Gene Expression Datasets...

In miracum/clearly-sigident.func: Sigident Functional Analysis

Perform Enrichtment Analysis in Gene Expression Datasets Derived from MicroArrays

Description

One function to perform gene enrichment analysis.

Usage

sigidentEnrichment(
  mergedset,
  mergeset,
  idtype,
  diagnosis,
  species,
  org_db,
  organism,
  pathwayid,
  plotdir = "./plots/",
  csvdir = "./tables/"
)

Arguments

mergedset	A large merged Expression Data set. The output of the funtion 'sigident.preproc::load_geo_data()'.
mergeset	A matrix of merged expression sets (rows = genes, columns = samples). The output of the funtion 'sigident.preproc::load_geo_data()'.
idtype	A character string. The type of ID used to name the genes. One of 'entrez' or 'affy' intended to use either entrez IDs or affy IDs. Caution: when using entrez IDs, missing and duplicated IDs are being removed!
diagnosis	A vector of integers, holding the binary outcome variable (0 = "Control", 1 = "Target").
species	A character string indicating the sample's species. Currently supported: "Hs".
org_db	A character string indicating the OrgDb. Currently supported: "org.Hs.eg.db".
organism	A character string indicating the organism. Currently supported: "hsa".
pathwayid	A character string indicating the pathway to show in the enrichment analysis. Currently supported: "hsa04110".'
plotdir	A character string. Path to the folder to store resulting plots. Default: "./plots/".
csvdir	A character string. Path to the folder to store output tables. Default: "./tables/".

miracum/clearly-sigident.func documentation built on June 28, 2022, 3:16 p.m.