Synthetic_Doublets: Synthetic Doublets

In EDePasquale/DoubletDecon: A Package to Identify Doublets and Doublet Clusters Based on Deconvolution Analysis and Unique Gene Expression

Description

This function creates synthetic doublets by averaging gene expression profiles from each combination of clusters to generate deconvolution profiles for each type of doublet.

Usage

Synthetic_Doublets(data, groups, groupsMedoids, newMedoids, num_doubs,
  log_file_name, only50, location)

Arguments

data	Processed data from Clean_Up_Input (or Remove_Cell_Cycle).
groups	Processed groups file from Clean_Up_Input.
groupsMedoids	New groups file based on blacklisted clusters from Blacklist_Groups
newMedoids	New combined medoids from Blacklist_groups.
num_doubs	The user defined number of doublets to make for each pair of clusters
log_file_name	used for saving run notes to log file
only50	use only synthetic doublets created with 50%/50% mix of parent cells, as opposed to the extended option of 30%/70% and 70%/30%, default is TRUE.

Value

averagesAverages = average deconvolution profiles for each combination of cell types.

doubletCellsInput2 = deconvolution profiles for synthetic doublet cells (for quality control).

EDePasquale/DoubletDecon documentation built on Dec. 3, 2020, 10:44 p.m.