infer: Main function of iSpatial

In Czh3/iSpatial: infer transcriptome-wide spatial expression via integration of scRNA and spRNA

Main function of iSpatial

Description

This function integrates scRNA-seq and spatial transcriptome. With limited genes in merFISH/SeqFISH, iSpatial infer/enhance all genes from scRNA-seq. Finally, this function generates spatially expression of all genes.

Usage

infer(
  spRNA,
  scRNA,
  dims = 1:30,
  k.neighbor = 30,
  infered.assay = "enhanced",
  weighted.KNN = TRUE,
  RNA.weight = 0.5,
  n.core = 8,
  correct.spRNA = FALSE,
  correct.scRNA = FALSE,
  correct.weight.NN = 0.2,
  correct.neighbor = 5
)

Arguments

spRNA	seurat object of spatial transcriptome data. Should contain normalized data. Run Seurat::NormalizeData or others.
scRNA	seurat object of single cell RNA-seq data. Should contain normalized data. Run Seurat::NormalizeData or others.
dims	which dimensions to use when find the nearest neighbors
k.neighbor	number of neighbors to use when infer the expression
infered.assay	names of output assay in seurat object
weighted.KNN	we use a dynamics weight to assign scRNA values to spRNA. The dynamics weight based on the correlation between scRNA cell and spRNA cell.
RNA.weight	the weight of scRNA-seq expression when genes detected both in spRNA and scRNA. RNA.weight should be 0 to 1. The inferred expression = (1 - RNA.weight) * spRNA + RNA.weight * scRNA.
n.core	number of CPU cores used to parallel.
correct.spRNA	Whether to stabilize expression in spRNA.
correct.scRNA	Whether to stabilize expression in scRNA.
correct.weight.NN	weight of nearest neighbors to correct expr.
correct.neighbor	number of nearest neighbors used to correct expr.

Value

returns a seurat object with inferred expression in infered.assay.

Czh3/iSpatial documentation built on Sept. 15, 2022, 10:32 p.m.