compartmentData: Calculate enrichment of subcellular compartment

In JoWatson2011/subcellularvis: What the Package Does (One Line, Title Case)

Calculate enrichment of subcellular compartment

Description

Calculate enrichment of subcellular compartment

Usage

compartmentData(
  genes,
  bkgd = NULL,
  id_type = c("SYMBOL", "UNIPROT"),
  aspect = c("Whole cell", "Endosomal system"),
  subAnnots = F,
  organism = c("Human", "Mouse", "Drosophila", "Yeast", "Rat", "Xenopus"),
  annotationSource = c("Gene Ontology", "Human Protein Atlas"),
  significanceThresh = 0.05
)

Arguments

genes	input genes (HGNC symbol) as character vector
bkgd	background population. Defaults to size of species library
id_type	Character; either "SYMBOL" or "UNIPROT", relating to identifier type of gene list.
aspect	Character; either "Whole cell" or "Endosomal system. Latter will calculate enrichment within endosomal system. system?
subAnnots	Logical; Calculate enrichment on all terms, not summarised
organism	One of "Human", "Mouse", "Drosophila", "Yeast", "Rat", "Xenopus"
annotationSource	Annotation source, Gene Ontology or (if organism = "Human") the Human Protein Atlas
significanceThresh	Threshold for FDR statistical significance. Default is 0.05

Value

data frame

JoWatson2011/subcellularvis documentation built on June 23, 2022, 2:09 p.m.