celltrek_dist: Calculate the RF-distance between sc and st

In navinlabcode/CellTrek: Spatial Charting of Single Cell Transcriptomes in Tissues

Calculate the RF-distance between sc and st

Description

Calculate the RF-distance between sc and st

Usage

celltrek_dist(
  st_sc_int,
  int_assay = "traint",
  reduction = "pca",
  intp = T,
  intp_pnt = 10000,
  intp_lin = F,
  nPCs = 30,
  ntree = 1000,
  keep_model = T
)

Arguments

st_sc_int	Seurat traint object
int_assay	Name of integration assay
reduction	Dimension reduction method used, usually pca
intp	If TRUE, do interpolation
intp_pnt	Interpolation point number
intp_lin	If TRUE, use linear interpolation
nPCs	Number of PCs used for CellTrek
ntree	Number of trees in random forest
keep_model	If TRUE, return the trained random forest model

Value

A list of 1. celltrek_distance matrix; 2. trained random forest model (optional)

Examples

dist_test <- celltrek_dist(st_sc_int=st_sc_int, int_assay='traint', reduction='pca', intp = T, intp_pnt=10000, intp_lin=F, nPCs=30, ntree=1000, keep_model=T)

navinlabcode/CellTrek documentation built on April 15, 2022, 8:04 a.m.