SyntheticDoublets: Synthetic Doublets

Description Usage Arguments Value

View source: R/SyntheticDoublets.R

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

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SyntheticDoublets(
  data,
  groups,
  groupsMedoids,
  newMedoids,
  num_doubs,
  only50,
  location,
  seed
)

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

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.

location

Directory where output should be stored

seed

Set a random seed.

Value

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

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


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