SpatialDE: Statistical Test to Identify Genes with Spatial Patterns

In estfernan/boost: Bayesian Modeling of Spatial Transcriptomics Data

Statistical Test to Identify Genes with Spatial Patterns

Description

SpatialDE is a method to identify and characterize spatially variable (SV) genes via a statistical test.

Usage

SpatialDE(norm.expr, spots, gene.name = NULL)

Arguments

norm.expr	A numeric vector p of length n that denotes the relative gene expression levels. Each entry is a numeric value that denotes the normalized gene count at spot i.
spots	An n-by-2 numeric matrix T to represent the geospatial profile, where each row indicates the spot location in the grid.
gene.name	A character string that specifies the name of the gene passed. To be used when storing the results. The default value is NULL to keep the gene expression levels unnamed.

Details

This method builds on Gaussian process regression, a class of models. For a given gene, the expression variability is decomposed into spatial and non-spatial components, using two random effect terms: a spatial variance term that parametrizes gene expression covariance by pairwise distances of samples, and a noise term that models non-spatial variability. The ratio of the variance explained by these two components quantifies the Fraction of Spatial Variance (FSV). Significant SV genes can be identified by comparing this full model to a model without the spatial variance component.

See https://bioconductor.org/packages/release/bioc/html/spatialDE.html for more information.

Value

SpatialDE returns an object of class "SpatialDE". The function base::print() i.e., print.SpatialDE(), can be used to print a summary of the results.

An object of class "SpatialDE" is a list containing the following components:

call	the function call in which all of the specified arguments are specified by their full names.
model	the name of statistical model or technique.
gene.name	the name of gene evaluated.
summary	a summary table that contains a summary of the model.
measures	the estimated p-value.
time	the execution time of the function.

References

Corso D, Malfait M, Moses L (2021). spatialDE: R wrapper for SpatialDE. doi: 10.18129/B9.bioc.spatialDE, R package version 1.0.0, http://www.bioconductor.org/packages/spatialDE.

Svensson V, Teichmann SA, Stegle O (2018). "SpatialDE: identification of spatially variable genes." Nature Methods, 15(5), 343–346. ISSN 1548-7105, doi: 10.1038/nmeth.4636, https://www.nature.com/articles/nmeth.4636.

See Also

normalize.st() for normalizing the expression levels; print.SpatialDE() for printing a summary of results to console.

Examples

library(boost)

## load sample dataset
data(mob)

## scale gene expression levels and extract one gene
mob.t <- normalize.st(mob, scaling.method = "TSS")
g     <- mob.t[, "Apoe"]

## run the statistical test
res <- SpatialDE(g, mob.spots, gene.name = "Apoe")
print(res)

estfernan/boost documentation built on June 24, 2022, 12:20 a.m.