scGO: scGO

In ncrna/Yeskit: Yet Another Single-Cell Analysis Toolkit (Yeskit)

scGO

Description

GO annotation for single-cell

Usage

scGO(
  object = NULL,
  key = NULL,
  clusters = NULL,
  logFC = 0.25,
  only.pos = TRUE,
  reference = "human",
  extra = NULL
)

Arguments

object	Seurat object
key	Keyword where DGEs are stored
clusters	A vector of clusters, default clusters=NULL
logFC	A positive value to set the cutoff of logFC
only.pos	Only up-regulated genes are taken into account, default only.pos=TRUE
reference	Reference organism to set ['human' or 'mouse'], default reference = 'human'
extra	Extra slot used to fetch DGEs

Value

A list object that stored GO results.

References

Inspired by Yuan et al, Methods in Molecular Biology (2019)

Examples

data("H3N2_small")
require(topGO)
x <- scGO(object = H3N2_small,
  key = "Infected_vs_Bystander", 
  logFC = 0.25,
  only.pos = FALSE,
  reference = "human"
)
head(x)

ncrna/Yeskit documentation built on Nov. 4, 2024, 10:32 p.m.