FindMarkers: Differential expression testing between 2 specified groups of...

In mgildea87/CVRCFunc: Functions for CVRC bioinformatics

Differential expression testing between 2 specified groups of cells via pseudobulking and DESeq2

Description

Differential expression testing between 2 specified groups of cells via pseudobulking and DESeq2

Usage

FindMarkers(
  seurat,
  clus_ident,
  group_1,
  group_2,
  sample_ident,
  expfilt_counts = 1,
  expfilt_freq = 0.5,
  out_dir = "FindMarkers",
  alpha = 0.1
)

Arguments

seurat	A Seurat object
clus_ident	Identity for clusters. Normally 'seurat_clusters' but can be any identity
group_1	Identity of cells within clus_ident to compare
group_2	Identity of cells within clus_ident to compare
sample_ident	Sample identities. Identity class that indicates how to partition samples
expfilt_counts	genes with less than expfilt_counts in expfilt_freq * sample number will be removed from DESeq2 model. 1 by default.
expfilt_freq	genes that have greater than expfilt_counts in greater than expfilt_freq fraction of cells will be kept for the DESeq2 model. 0.5 by default
out_dir	Name of output directory
alpha	FDR adjusted p-value threshold for significance in plotting. 0.1 by default.

Value

.csv files with marker genes per clus_ident. .pdf files with diagnostic plots

mgildea87/CVRCFunc documentation built on Nov. 9, 2024, 7:39 p.m.