scPathogenDGE: Find differentially expressed genes by species for each...

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

Find differentially expressed genes by species for each clusters

Description

Find differentially expressed genes by species for each clusters

Usage

scPathogenDGE(
  object = NULL,
  species.by = NULL,
  clusters = NULL,
  min.cells = 20,
  min.pct = 0.1,
  logFC = 0.25
)

Arguments

object	Seurat object
species.by	String of species to divid cells into two groups (Positive / Negative)
clusters	Clusters specified for DGE, default clusters=NULL, means all clusters will be evaluated
min.cells	Minimum number of cells for DGE in any of the two groups, default min.cells=20
min.pct	Genes expressed in any of the two groups with a minium cell fraction (min.pct) are reserved for DGE, default min.pct=0.1
logFC	A positive value to set the cutoff of logFC, default logFC=0.25

Value

DGE table

References

Inspired by Stuart and Butler et al, Cell (2019)

Examples

data("H3N2_small")
x <- scPathogenDGE(object = H3N2_small, 
  species.by = "H3N2",
  min.cells = 5,
  min.pct = 0.1,
  logFC = 0.25,
)
head(x)

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