jointDistance: jointDistance.Seurat

In WilsonImmunologyLab/LinQseq: Integrate information from both transcriptome and cell surface protein signals to better identify cell heterogeneity

Description

If input seurat object, will calculate cell-cell pairwise distances for RNA and ADT separately, then calculate the joint cell-cell pairwise distances. It alao can calculate joint distances for any two dist objects

Usage

## S3 method for class 'Seurat'
jointDistance(
  object,
  dims = 20,
  beta = 0.5,
  model = "LP",
  keep.rna = TRUE,
  keep.adt = TRUE,
  sigmoid.n = 10,
  sigmoid.k = 0.5,
  precision.mode = TRUE,
  c = NULL
)

## Default S3 method:
jointDistance(object, dist1 = NULL, dist2 = NULL, beta = 1, model = "LP")

jointDistance(object, ...)

Arguments

object	(For Seurat) Seurat object
dims	(For Seurat) number of PCs used for RNA data. Default is 20
beta	(For default) For L1 model, use beta to balence contributions from RNA and ADT in the joint distances (0 <= beta <= 1). Default value is 0.5, indicate L1 modal will treat RNA and ADT equally. higher beta will increase the contribution of RNA
model	(For default) Norm model for distance integration. Default model is L-infinite model. Another option is L1 model.
dist1	(For default) dist object of first assay
dist2	(For default) dist object of second assay

WilsonImmunologyLab/LinQseq documentation built on Dec. 29, 2021, 8:15 p.m.