PoweREST_gene {PoweREST}R Documentation

Bootstrap resampling and power estimation for one single gene

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 upon one gene specified by the user. Users can specify the test they would like to perform for the DE analysis in '...'. Note that the results are not multiple testing corrected, therefore should be interpreted carefully.

Usage

PoweREST_gene(Seurat_obj,cond,replicates=1,spots_num,
gene_name,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.

gene_name

Specify the name of gene for power calculation.

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 gene's name.

Author(s)

Lan Shui lshui@mdanderson.org


[Package PoweREST version 0.1.0 Index]