SpatialGradientScreening-class: The 'SpatialGradientScreening' - Class

In kueckelj/SPATA2: A Toolbox for Spatial Expression Analysis

The SpatialGradientScreening - Class

Description

S4 class that contains input for and output of spatial gradient screening implementation spatialAnnotationScreening() and spatialTrajectoryScreening().

Details

The following classes are derivates of this class: SpatialAnnotationScreening, SpatialTrajectoryScreening.

Slots

coordinates

data.frame. A data.frame as obtained by getCoordsDfSA() or getCoordsDfST(), respectively, with the setup used for the screening.

models

data.frame. A data.frame in which columns correspond to the modeled gradients used for the model fitting.

qc

list. A named list that contains results from the quality control steps. Reserved list slots are:

• cf Numeric value. The correction factor used to adjust the span.

• est_R2 List. Results from estimating the overal R2 between noise and total variation.

• zero_infl_vars Character vector. Names of variables that have been identified as zero inflated.

results

A named list that contains the screening results. Reserved list slots are:

• significance Data frame with results from the identification of non-random gradients.

• model_fits Data frame with results from gradient ~ model fits.

sample

Character value. The name of the SPATA2 object with which the screening was conducted.

set_up

A list of parameters required to reproduce the set up of the screening.

kueckelj/SPATA2 documentation built on Feb. 27, 2025, 1:45 p.m.