group_cl: Assign clusters to a group

In AllenInstitute/scrattch.hicat: Hierarchical Iterative Clustering Analysis for Transcriptomic data

Assign clusters to a group

Description

This function assigns each cluster to a predefined set of classes (exc, inh, glia, donor, outlier) using test.genes (default GAD1, GAD2, SLC17A7, SLC17A6). Later iterations of the function will allow for user-defined classes and genes.

Usage

group_cl(
  anno,
  cluster,
  norm.dat,
  select.cells = colnames(norm.dat),
  neun.thresh = 0.5,
  neun.colname = "facs_population_plan",
  neun.val = "NeuN-pos",
  test.genes = c("GAD1", "GAD2", "SLC17A7", "SLC17A6"),
  expr.th = 3,
  prop.th = c(0.5, 0.5, 0.2, 0.2),
  outlier.cl = NULL,
  donor.cl = NULL
)

Arguments

anno	anno dataframe which must include column names listed in 'neun.colname' "cluster" is added from 'cluster' parameter below.
cluster	clusters labels for all cells along with sample_id as their names
norm.dat	expression dataframe with columns as cells and rows as gene names and cpm normalized
select.cells	column names of norm.dat
neun.thresh	fraction of cells expressing NeuN to be considered NeuN positive (default is 0.5)
neun.colname	column name in anno with the Neun information
neun.val	value corresponding to non-neuronal marker in neun.colname in anno
test.genes	genes used to define cell classes (default is GAD1, GAD2, SLC17A7, SLC17A6)
expr.th	expression threshold for detecting test genes
prop.th	proportion threshold of detected genes by cluster (default is 0.5, 0.5, 0.2, 0.2)
outlier.cl	vector of clusters previously defined as "outlier" (default is NULL)
donor.cl	vector of clusters previously defined as "donor" (default is NULL)

Value

gives the clusters names in each class (exc, inh, glia, donor, outlier) as a list

AllenInstitute/scrattch.hicat documentation built on June 6, 2024, 5:31 a.m.