FindMarkersBulk: Find all markers via pseudobulking and DESeq2

In mgildea87/CVRCFunc: Functions for CVRC bioinformatics

Find all markers via pseudobulking and DESeq2

Description

Find all markers via pseudobulking and DESeq2

Usage

FindMarkersBulk(
  seurat,
  clus_ident,
  sample_ident,
  expfilt_counts = 1,
  expfilt_freq = 0.5,
  n_top_genes = 50,
  pct.in = 25,
  out_dir = "FindMarkersBulk_outs",
  alpha = 0.1,
  assay = "RNA"
)

Arguments

seurat	A Seurat object
clus_ident	Identity for clusters. Normally 'seurat_clusters' but can be any identity
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 mode. 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
n_top_genes	number of top genes per cluster to save and make a heatmap with
pct.in	Filter threshold for top marker genes per cluster. For a given gene and cluster, if the fraction of cells with counts is less than pct.in it is removed from top_markers.
out_dir	Name of output directory
alpha	FDR adjusted p-value threshold for significance in plotting. 0.1 by default.
assay	Which assay to use. RNA by default. I added this parameter to enable use of ADT data when desired.

Value

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

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