| Title: | E-Statistics for Seurat Objects |
|---|---|
| Description: | R version of 'scperturb' tool for single-cell perturbation analysis. Contains wrappers for performing E-statistics for Seurat objects. More details on the method can be found in Peidli et al. (2023) <doi:10.1101/2022.08.20.504663> and in Székely and Rizzo (2004). |
| Authors: | Stefan Peidli |
| Maintainer: | Stefan Peidli <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.1.0 |
| Built: | 2025-03-16 04:20:58 UTC |
| Source: | https://github.com/cran/scperturbR |
Computes pairwise E-distances on a Seurat object. Computes E-distance between all groups in a Seurat object in space given by reduction.
edist( seurat_object, groupby = "perturbation", reduction = "pca", sample_correction = FALSE, verbose = TRUE )edist( seurat_object, groupby = "perturbation", reduction = "pca", sample_correction = FALSE, verbose = TRUE )
seurat_object |
An object of class Seurat. |
groupby |
An object of class character. Points to the column in the Seurat object's meta data that contains the group labels. |
reduction |
An object of class character. The reduction / embedding in seurat_object that is used to compute the E-distance in. |
sample_correction |
An object of class logical. If TRUE, the E-distances are corrected for sample size. Will make it not a proper distance, leads to negative values. |
verbose |
An object of class logical. If TRUE, prints messages. Default is TRUE. |
Returns an object of class data.frame. For each group contains the E-test p-value and the E-distance to control group.
# Add some code illustrating how to use the function# Add some code illustrating how to use the function
Performs E-testing on a Seurat object. Computes E-test statistics for each group in a Seurat object, using the E-distance in space given by reduction to the group defined by control.
etest( seurat_object, groupby = "perturbation", control = "control", reduction = "pca", verbose = TRUE, permutations = 1000 )etest( seurat_object, groupby = "perturbation", control = "control", reduction = "pca", verbose = TRUE, permutations = 1000 )
seurat_object |
An object of class Seurat. |
groupby |
An object of class character. Points to the column in the Seurat object's meta data that contains the group labels. |
control |
An object of class character. The group that is used as the control. |
reduction |
An object of class character. The reduction / embedding in seurat_object that is used to compute the E-distance in. |
verbose |
An object of class logical. If TRUE, prints messages. Default is TRUE. |
permutations |
An object of class integer. The number of permutations used to compute the p-value. Default is 1000. |
Returns an object of class data.frame. For each group contains the E-test p-value and the E-distance to control group.
# Add some code illustrating how to use the function# Add some code illustrating how to use the function