BlacklistGroups: Blacklist Groups

In lyc-1995/DoubletDeconSeurat: Seurat wrappers with DoubletDecon

Description

This function is used for the calculation of blacklisted medoids and groups. It calculates medoids, performs medoid correlations and creates the binary correlation table between medoids, otherwise known as the blacklist. It makes a blacklist heatmap. It makes new medoids based on blacklisted combined clusters and a new groups file based on the blacklisted combined clusters.

Usage

BlacklistGroups(data, groups, rhop, centroid_flag, log_file_name)

Arguments

data	Processed data from CleanUpInput (or RemoveCellCycle)
groups	Processed groups file from CleanUpInput
rhop	x in mean+x*SD to determine upper cutoff for correlation in the blacklist. Default is 1.
centroid_flag	use centroids if data is sparse
log_file_name	used for saving run notes to log file

Value

newMedoids - new medoids data.frame for the new combined blacklisted clusters.

newGroups - new groups file containing cluster assignment based on new combined blacklisted clusters.

lyc-1995/DoubletDeconSeurat documentation built on March 8, 2020, 5:47 a.m.