check_donor: Find donor clusters

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

Find donor clusters

Description

This function identifies clusters that are nearly exclusively expressed in one donor. Currently it is hard-coded to define clusters with >90 or >50 function iterations will include these options as parameters.

Usage

check_donor(
  anno,
  cluster,
  norm.dat,
  select.cells = names(cluster),
  keep.cl = NULL,
  meta1_area = "roi",
  meta2_donor = "external_donor_name",
  plot = TRUE,
  plot.path = "output/"
)

Arguments

anno	anno dataframe which must include column names listed in 'neun.colname' 'meta1_area' and 'meta2_donor' below. "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 nmaes of norm.dat
keep.cl	clusters to definitely keep in analysis (e.g., to exclude from consideration as a donor cluster) default is NULL
meta1_area	The metadata column that contains information about the area (e.g. cortical region and layer). default is "roi"
meta2_donor	The metadata column that contains information about the donor. default is "external_donor_name"
plot	default is TRUE
plot.path	path of plot, default is "./output/"

Value

Gives cluster ids vs donor expression/region heatmap

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