Assign clusters to a group — group

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.

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