View source: R/human_functions.R
check_donor | R Documentation |
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.
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/"
)
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/" |
Gives cluster ids vs donor expression/region heatmap
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