CARD_SCMapping: Extension of CARD into performing single cell Mapping from...

In YingMa1993/CARD: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

Extension of CARD into performing single cell Mapping from non-single cell spatial transcriptomics dataset.

Description

Extension of CARD into performing single cell Mapping from non-single cell spatial transcriptomics dataset.

Usage

CARD_SCMapping(CARD_object, shapeSpot = "Square", numCell, ncore = 10)

Arguments

CARD_object	CARD object create by the createCARDObject function.
shapeSpot	a character indicating whether the sampled spatial coordinates for single cells locating in a Square-like region or a Circle-like region. The center of this region is the measured spatial location in the non-single cell resolution spatial transcriptomics data. The default is "Square", the other shape is "Circle"
numCell	a numeric value indicating the number of single cells in each measured location, we suggest 20 for ST technology, 7 for 10x Viisum and 2 for Slide-seq
ncore	a numeric value indicating the number of cores used to accelerating the procedure

Value

Returns a SingleCellExperiment SCE object with the mapped expression at single cell resolution and the spatial location information of each single cell

YingMa1993/CARD documentation built on Feb. 14, 2024, 12:24 p.m.