The spata2- Class

The spata2- Class

Value

S4 object

Slots

autoencoder

A list in which the results of neural network denoising is stored.

coordinates

A data.frame containing information about every barcode-spot. Must contain the variables:

barcodes

Character. The barcode-sequences (+ the sample belonging) of every barcode spot.

sample

Character. The sample belonging of every barcode-spot.

x

Numeric. The x-coordinates of every barcode.

y

Numeric. The y-coordinates of every barcode.

data

See documentation for S4-object 'data'

dea

A list in which every slot is named according to a discrete feature for which differential gene expression analysis has been conducted (via findDeGenes()). Every slot contains a data.frame (output of Seurat::FindAllMarkers()).

dim_red

See documentation for S4-object 'dim_red'

fdata

A data.frame containing the additionally computed features. Must contain the variables:

barcodes

Character. The barcode-sequences (+ the sample belonging) of every barcode spot.

sample

Character. The sample belonging of every barcode-spot.

image

A list of images named according to the samples the object contains.

samples

Character value. Contains the sample names.

scvelo

Currently not in use.

trajectories

A list named according to the samples the object contains. Each slot in that list contains another list of all 'spatial_trajectory'-objects created for that sample.

used_genesets

A data.frame containing the defined gene-sets. Must contain the variables:

ont

Character. The gene-set name.

gene

Character. The belonging genes.

version

A list of four slots denoting the version of SPATA under which the object has been created.

compatibility

A list of miscellaneous information that mainly ensures compatibility between different platforms.