WriteMetaCells: Generates metacells from the given Seurat object. Rquires...

In califano-lab/PISCES: Protein Activity Inferecne in Single Cells

Generates metacells from the given Seurat object. Rquires that the 'PISCESgexp' assay has been added. By default, uses the 'pisces.clust' metadata to group clusters. This can be overrided with the 'clust.vec' argument. If clust.vec is 'NA', then the entire matrix will be used.

Description

Generates metacells from the given Seurat object. Rquires that the 'PISCESgexp' assay has been added. By default, uses the 'pisces.clust' metadata to group clusters. This can be overrided with the 'clust.vec' argument. If clust.vec is 'NA', then the entire matrix will be used.

Usage

WriteMetaCells(
  pisces.obj,
  file.path = ".",
  proj.name = "",
  clust.vec = NULL,
  num.neighbors = 5,
  subset = 250,
  min.samps = 500
)

Arguments

pisces.obj	A Seurat object with the PISCESgexp assay.
proj.name	File name preface
clust.vec	Optional clustering vector object.
num.neighbors	Number of neighbors to use in metacells. Default of 5.
subset	Number of cells to subset to. Default of 250. No subsetting if set equal to NULL.
min.samps	Minimum number of samples in a cluster required for meta cells. Default of 500.
out.dir	Output directory for metacell matrices to be written to.

califano-lab/PISCES documentation built on Jan. 11, 2023, 5:34 a.m.