celltype_effects {BUSseq}R Documentation

Obtain the Cell-type Effects from the Output of the BUSseq_MCMC Function

Description

The function gives the estimated cell-type effects in the output SingleCellExperiment object.

Usage

celltype_effects(sce_BUSseqfit)

Arguments

sce_BUSseqfit

An output SingleCellExperiment object by the function BUSseq_MCMC.

Value

beta.est

The estimated cell-type effects, a G by K matrix, whose [g,k] element is the effects of cell type k on gene g compared with the first cell type. Note that the first column is zero as the first cell type is taken as the baseline cell type.

Author(s)

Fangda Song

References

Song, Fangda, Ga Ming Angus Chan, and Yingying Wei. Flexible experimental designs for valid single-cell RNA-sequencing experiments allowing batch effects correction. Nature communications 11, no. 1 (2020): 1-15.

Examples

# "BUSseqfits_example" is an example output
BUSseqfits_example
beta.est <- celltype_effects(BUSseqfits_example)

[Package BUSseq version 0.99.18 Index]