check_neun: Check whether clusters are Neun+ or Neun-

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

Check whether clusters are Neun+ or Neun-

Description

This function is very specific to brain cell/nuclear data where Neun is used as a stain for neuronal vs. non-neuronal identity. This function determine's whether a cluster is predicted to be neuronal or non-neuronal based on expression of Neun.

Usage

check_neun(
  anno,
  cluster,
  neun.thresh = 0.5,
  neun.colname = "facs_population_plan",
  neun.val = "NeuN-pos"
)

Arguments

anno	anno dataframe which must include column name listed in 'neun.colname'
cluster	cluster labels for all cells along with sample_id as their names
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

Value

returns all the clusters and true/false of whether they are Neun positive

AllenInstitute/scrattch.hicat documentation built on Oct. 20, 2023, 6:55 a.m.