PoweREST {PoweREST}R Documentation

Bootstrap resampling and power calculation upon ST data

Description

This function performs bootstrap resampling upon a Seurat subject under each condition to resemble the real dataset which allows the exact power calculation, and perform DE analysis. Users can specify the test they would like to perform for the DE analysis in '...' which should not contain min.pct and logfc.threshold or other parameters attempt to pre-filter genes, as we specify min.pct and logfc.threshold as 0s to calculate power for all the genes available. Therefore it may take one night to run if the ST data owns over thousands of genes. To speed up this process, one may want to try function 'PoweREST_subset' where the pre-filter of genes are included in this process.

Usage

PoweREST(Seurat_obj,cond,replicates=1,spots_num,
iteration=100,random_seed=1,pvalue=0.05,...)

Arguments

Seurat_obj

A Seurat object.

cond

The name of the variable that indicates different conditions which is also stored in the meta.data of the Seurat_obj and should be in character type.

replicates

The number of sample replicates per group.

spots_num

The number of spots per replicate.

iteration

The number of iterations of the resampling.

random_seed

To set a random seed.

pvalue

The pvalue that will be considered significant.

...

DE test to use other than the default Wilcoxon test.

Value

A list of values containing the power, average log2FC and percentage of spots detecting the gene among the resampling data, the replicate value and the spots number per slice specified by the user and corresponding genes' name.

Author(s)

Lan Shui lshui@mdanderson.org


[Package PoweREST version 0.1.0 Index]