scRNA_markers_assign: scRNA Marker Based Cell Type Assignments

In Jerby-Lab/opipes: What the Package Does (One Line, Title Case)

scRNA Marker Based Cell Type Assignments

Description

Using gene expression markers, unsupervised clusters, and gene expression, assign the likely celltype to those clusters

Usage

scRNA_markers_assign(
  r,
  cell.clusters,
  cell.sig,
  immune.markers,
  non.immune.cell.types = c("Endothelial", "CAF", "Malignant"),
  EM.flag = F,
  OE.type = "V1",
  test.type = "ttest",
  minZ = 10,
  subsample = T
)

Arguments

r	data list including the gene expression data
cell.clusters	a n-length list to where n is the number of cells
cell.sig	cell type signatures (list of lists of markers associated with each cell-type, default exists)
immune.markers	immune markers (default exists)
non.immune.cell.types	which cell types are not immune cell types?
EM.flag	run EM? (default = F)
OE.type	which version of overall-expression to calculate (default = "V1")
test.type	which kind of test to test marker significance between clusters
minZ	minimum significance cutoff to assign a cell-type (default = 10)

Value

a list with objects named "c" and "m" corresponding to your subsampled counts and metadata

Jerby-Lab/opipes documentation built on Oct. 7, 2022, 12:28 p.m.