createCARDObject: Create the CARD object

In YingMa0107/CARD: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

Create the CARD object

Description

Create the CARD object

Usage

createCARDObject(
  sc_count,
  sc_meta,
  spatial_count,
  spatial_location,
  ct.varname,
  ct.select,
  sample.varname,
  minCountGene = 100,
  minCountSpot = 5
)

Arguments

sc_count	Raw scRNA-seq count data, each column is a cell and each row is a gene.
sc_meta	data frame, with each row representing the cell type and/or sample information of a specific cell. The row names of this data frame should match exactly with the column names of the sc_count data
spatial_count	Raw spatial resolved transcriptomics data, each column is a spatial location, and each row is a gene.
spatial_location	data frame, with two columns representing the x and y coordinates of the spatial location. The rownames of this data frame should match eaxctly with the columns of the spatial_count.
ct.varname	character, the name of the column in metaData that specifies the cell type annotation information
ct.select	vector of cell type names that you are interested in to deconvolute, default as NULL. If NULL, then use all cell types provided by single cell dataset;
sample.varname	character,the name of the column in metaData that specifies the sample information. If NULL, we just use the whole as one sample.
minCountGene	Minimum counts for each gene
minCountSpot	Minimum counts for each spatial location

Value

Returns CARD object with filtered spatial count and single cell RNA-seq dataset.

YingMa0107/CARD documentation built on Feb. 14, 2024, 12:23 p.m.