All-Cluster-Marker: Find All Cluster Markers

In bioinfoDZ/RISC: Robust Integration of Single-Cell RNA-Seq Datasets

Find All Cluster Markers

Description

This function depends on "scMarker" function by using the same criteria, and generates markers for all the clusters. Here, if the cell number of any cluster is less than 10 , RISC will skip this cluster and not detect its cluster markers in the default parameters.

Usage

AllMarker(
  object,
  positive = TRUE,
  frac = 0.25,
  log2FC = 0.5,
  Padj = 0.05,
  latent.factor = NULL,
  min.cells = 25L,
  method = "QP",
  ncore = 1
)

Arguments

object	RISC object: a framework dataset.
positive	Whether only output the cluster markers with positive log2FC.
frac	A fraction cutoff, the marker genes expressed at least a cutoff fraction of all the cells.
log2FC	The cutoff of log2 Fold-change for differentially expressed marker genes.
Padj	The cutoff of the adjusted P-value.
latent.factor	The latent factor from coldata, which represents number values or factors, and only one latent factor can be inputed.
min.cells	The threshold for the cell number of valid clusters.
method	Which method is used to identify cluster markers, three options: 'NB' for Negative Binomial model, 'QP' for QuasiPoisson model, and 'Wilcox' for Wilcoxon Rank Sum and Signed Rank model.
ncore	The multiple cores for parallel calculating.

Details

Because log2 cannot handle counts with value 0, we use log1p to calculate average values of counts and log2 to format fold-change.

bioinfoDZ/RISC documentation built on March 30, 2024, 9:19 p.m.