scPathogenGO: scPathogenGO annotation

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

scPathogenGO annotation

Description

GO annotation for scPathogenDGE results

Usage

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

Arguments

object	Seurat object
key	The DGEs are stored in object@misc$key
species	Species which is used to divid cells into two groups
clusters	A vector of clusters, default all clusters will be used
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'

Value

Table that stores scPathogenGO results

References

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

Examples

data("H3N2_small")
require(topGO)
x <- scPathogenGO(object = H3N2_small,
  key = "H3N2", 
  species = "H3N2",
  logFC = 0.25,
  only.pos = FALSE,
  reference = "human"
)
head(x)

ncrna/Yeskit documentation built on Oct. 27, 2023, 2:13 a.m.