CreateSpatialPCAObject: Create the SpatialPCA object with filtering and normalization...

In shangll123/SpatialPCA: Spatially Aware Dimension Reduction for Spatial Transcriptomics

Create the SpatialPCA object with filtering and normalization step.

Description

Create the SpatialPCA object with filtering and normalization step.

Usage

CreateSpatialPCAObject(
  counts,
  location,
  covariate = NULL,
  project = "SpatialPCA",
  gene.type = "spatial",
  sparkversion = "spark",
  numCores_spark = 1,
  gene.number = 3000,
  customGenelist = NULL,
  min.loctions = 20,
  min.features = 20
)

Arguments

counts	Gene expression count matrix (matrix), the dimension is m x n, where m is the number of genes and n is the number of locations.
location	Spatial location matrix (matrix), the dimension is n x d, n is the number of locations, d is dimensin of spatial coordinates, e.g. d=2 for locations on 2D space. The rownames of locations and the colnames of count matrix should be matched.
covariate	The covariates in experiments (matrix, if any covariate included), n x q, n is the number of locations, q is the number of covariates. The rownames of covariates and the rownames of locations should be matched.
project	Name of the project (for record keeping).
gene.type	The type of genes to be used: "spatial" for spatially expressed genes; "hvg" for highly variable genes; "custom" for user specified genes, default is "spatial".
sparkversion	In spatial gene selection, specify "spark" for small sample size data for higher detection power of spatial genes, "sparkx" for large sample size data for saving time and memory.
numCores_spark	If gene.type="spatial", specify the number of CPU cores in SPARK package to use when selecting spatial genes.
gene.number	The number of top highly variable genes if gene.selection=="hvg" (use all HVG genes if this number is not specified); number of top spatially expressed genes if gene.selection=="spatial" (use all significant spatially expressed genes if this number is not specified).
customGenelist	A list of user specified genes if gene.type=="custom".
min.loctions	The features (genes) detected in at least min.loctions number of loctions, default is 20.
min.features	The locations where at least min.features number of features (genes) are detected, default is 20.

Value

Returns SpatialPCA object, with filtered and normalized gene expression matrix and corresponding location matrix.

shangll123/SpatialPCA documentation built on April 17, 2024, 3:15 a.m.