runLISI: LISI analysis

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

LISI analysis

Description

LISI analysis

Usage

runLISI(
  lisi_label1 = "donor",
  lisi_label2 = "CellType",
  reference.celltypes.rds.file = "",
  integrative.umap.rds.files = "",
  integrative.method.names = "",
  point.size = 5,
  IsShowPlot = TRUE
)

Arguments

lisi_label1	The batch effect variable of interest such as 'batch' and 'donor'. Default 'donor'
lisi_label2	The variable name that represents ground truth or high AUC score cell type'. Default 'CellType'
reference.celltypes.rds.file	The RDS file name that contains cell type information.
integrative.umap.rds.files	The vector of file names that contain UMAP coordinate information generated by different integrative methods.
integrative.method.names	The vector of integrative method names represented in the same order as in 'integrative.umap.rds.files'.
point.size	The size of data points in the plot.
IsShowPlot	If TRUE, the function will show the plot. If not, it will return the lisi's scores.

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.