PrepDoubletDecon: Seurat V3 Pre Process

In lyc-1995/DoubletDeconSeurat: Seurat wrappers with DoubletDecon

Description

Pre-process Seurat V3 object for DoubletDecon

Usage

PrepDoubletDecon(
  object,
  assay = NULL,
  markers = NULL,
  top.n = 50,
  group.by = NULL,
  output.dir = NULL
)

Arguments

object	Seurat object which has been pre-processed with clustering and dimensional reduction
assay	Name of assay to pull the count data from; default is 'RNA'.
markers	Output of FindAllMarkers. If NULL, will recalculate it with default parameters.
top.n	Number of markers for the top_n function. Default is 50.
group.by	Name of one metadata columns to group cells by; If NULL, will use current identity.
output.dir	If set, save the output files to .txt format. Defauly is NULL.

Value

a list with three elements: newExpressionFile - Seurat expression file in ICGS format (ICGS genes) newFullExpressionFile - Seurat expression file in ICGS format (all genes) newGroupsFile - Groups file ICGS format

References

DePasquale, E. A., Schnell, D. J., Van Camp, P. J., Valiente-Alandí, Í., Blaxall, B. C., Grimes, H. L., ... & Salomonis, N. (2019). DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data. Cell reports, 29(6), 1718-1727.

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