SDEGS-class: The 'SDEGS'-class

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

The SDEGS-class

Description

S4 class that serves as a container for results of detection of spatially differentially expressed genes (SDEGs) as suggested by Zeng et al. 2023. Contains the results of findSDEGS()

Slots

coordinates

data.frame. Data.frame of four variables barcodes, x, y, bins_dist to visualize the testing set up.

dea_1v1

list. List of data.frames each containing the differentially expressed genes for the circle bin vs. Control according to which the slot containing the data.frame is named (as returned by Seurat::FindMarkers()).

dea_all

data.frame. Data.frame of DEA testing as returned by Seurat::FindAllMarkers().

spat_ann

SpatialAnnotation. The spatial annotation based on which the testing was conducted.

spatial_parameters

list. List of three slots named binwidth, distance, n_bins_dist as was set up using the corresponding parameters.

sample

character. Name of the sample to which the results belong.

References

This is an R-implementation of the approach suggested by Zeng, H., Huang, J., Zhou, H. et al. Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in a mouse model of Alzheimer's disease. Nat Neurosci 26, 430-446 (2023).

See Also

findSDEGS()

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.