createCARDfreeObject: 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

createCARDfreeObject(
  markerList,
  spatial_count,
  spatial_location,
  minCountGene = 100,
  minCountSpot = 5
)

Arguments

markerList	a list of marker genes, with each element of the list being the vector of cell type specific marker genes
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.
minCountGene	Minimum counts for each gene
minCountSpot	Minimum counts for each spatial location

Value

Returns CARDfree object with filtered spatial count and marker gene list.

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