cside_spase: Main function for detecting spatial allele-specific...

In lulizou/spASE: Detecting Allele-Specific Expression in Spatial Transcriptomics

Main function for detecting spatial allele-specific expression (ASE) patterns considering cell type mixtures.

Description

This function fits the spatial beta-binomial model with cell type mixtures.

Usage

cside_spase(myRCTD, df = 5, genes = NULL, cores = 1, verbose = F)

Arguments

myRCTD	RCTD object with maternalCounts and paternalCounts slots
df	integer, sets the number of degrees of freedom to use for the smoothing spline. Default is 5. Usually want to increase this or test multiple.
genes	optional vector of genes to run on. Good for testing things out.
cores	number of cores to use for parallelization. Default is 1.

Details

Fits the intercept-only model (only cell type effects) and the spatial model (non-parametric thin plate smoothing splines)

Value

If method is betabinomial or quasibinomial, a list containing the following output:

• results a data frame containing a summary of the results including p-values and q-values for goodness of spatial fit over baseline covariates provided

• fits a list of beta-binomial model fit objects for each gene

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lulizou/spASE documentation built on May 22, 2024, 5:24 a.m.