find_markers: Find marker genes for cell clusters

In huipan1973/ezscrnaseq: What the Package Does (One Line, Title Case)

Find marker genes for cell clusters

Description

Find marker genes for cell clusters using scran findMarkers

Usage

find_markers(
  sce,
  clusters,
  annot,
  block = NULL,
  lfc = 1,
  test.type = c("t", "wilcox", "binom"),
  direction = c("up", "down", "any"),
  pval.type = c("any", "all"),
  assay_type = c("logcounts", "counts", "corrected"),
  ncores = 1,
  fdr_cutoff = 0.25,
  prefix = NULL,
  write = TRUE
)

Arguments

sce	A SingleCellExperiment object containing expression values, usually counts.
clusters	Vector specify cell clusters.
annot	gene annotation.
block	Vector specify blocking.
lfc	Log fold-change.
test.type	String specifying the type of pairwise test to perform - a t-test with "t", a Wilcoxon rank sum test with "wilcox", or a binomial test with "binom".
direction	Direction of change.
pval.type	A string specifying how p-values are to be combined across pairwise comparisons for a given group/cluster.
assay_type	A string specifying which assay values to use, e.g., "counts" or "logcounts".
ncores	Number of cores.
fdr_cutoff	FDR cutoff for top marker genes.
prefix	Prefix for file name for the QC metrics histograms.
write	TRUE/FASLE for whether write the table of filtered cells.

Value

A data.frame for the statistics and annotation of top marker geness

huipan1973/ezscrnaseq documentation built on July 12, 2022, 9:36 p.m.