CalculateDoublets: CalculateDoublets

In bicciatolab/PoPsicleR: Pipeline of Preprocessing for Single Cell Experiment

CalculateDoublets

Description

Calculates, highlights and optionally removes doublets in the provided dataset. This function can be run twice sequentially, first time to explore doublets graphs and subsequently to set the appropriate threshold for doublets identification.

Usage

CalculateDoublets(UMI, method=c("scrublet","scDblFinder"), dbs_thr='none', dbs_rate=NULL, dbs_remove=TRUE, out_folder=getwd())

Arguments

UMI	Input UMI object generated either via previous popsicleR funtions or CalculateDoublets function
method	Method to use for doublets calculation. It can be "scrublet" or "scDblFinder". Default is "scrublet"
dbs_thr	Doublets threshold. Default is auto calculated. Used only if method = "scrublet"
dbs_rate	Expected doublets rate. Default is auto calculated. Used only if method = "scDblFinder"
dbs_remove	Remove doublets if TRUE. Default is TRUE
out_folder	Output folder. Default is the working directory

Details

CalculateDoublets returns two graphs in the "01.QC_Plots" folder:

the first (01h) allows the visualization of the cell doublets and of the doublet scores on a UMAP projection.

the second (01i), computed only if method = "scrublet", returns histograms of observed and simulated doublet score distributions and the value of the automatically detected threshold for the simulated doublet score.

Value

Returns a Seurat Object after doublets calculation.

If "dbs_remove = TRUE", cells labeled as doublets are removed from the object.

Author(s)

Jimmy Caroli, Francesco Grandi, Chengxiang Qiu

References

The main function used to identify doublets with Scrublet has been modified from the R code provided at https://rdrr.io/github/ChengxiangQiu/rscrublet/ by Chengxiang Qiu <[e-mail]> based on the method implemented in the python module Scrublet

Samuel L. Wolock, Romain Lopez, Allon M. Klein, "Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data" (2019). Cell System, Volume 8,–281-291–.e9,ISSN 2405-4712,https://doi.org/10.1016/j.cels.2018.11.005.

Germain PL, Lun A, Macnair W and Robinson MD. Doublet identification in single-cell sequencing data using scDblFinder. F1000Research (2021), 10:979 https://doi.org/10.12688/f1000research.73600.1

Examples

## first run using scrublet:
umi_object <- CalculateDoublets(umi_object, method = "scrublet", dbs_thr='none', dbs_remove=FALSE)

## second run using scrublet:
CalculateDoublets(umi_object, method = "scrublet", dbs_thr=0.22, dbs_remove=TRUE)

## first run using scDblFinder:
umi_object <- CalculateDoublets(umi_object, method = "scDblFinder", dbs_rate=NULL, dbs_remove=FALSE)

## second run using scDblFinder:
CalculateDoublets(umi_object, method = "scDblFinder", dbs_rate=0.22, dbs_remove=TRUE)

bicciatolab/PoPsicleR documentation built on May 7, 2024, 7:26 a.m.