location_batch_effects {BUSseq}R Documentation

Obtain the Location Batch Effects from the Output of the BUSseq_MCMC Function

Description

The function gives the estimated location batch effects in the output SingleCellExperiment object.

Usage

location_batch_effects(sce_BUSseqfit)

Arguments

sce_BUSseqfit

An output SingleCellExperiment object obtained from the function BUSseq_MCMC.

Value

nu.est

The estimated location batch effects, a G by B matrix, where [g,b] element is the location batch effect on gene g in the batch b compared with the first batch. Note that the first column is zero as the first batch is taken as the reference batch without batch effects.

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
nu.est <- location_batch_effects(BUSseqfits_example)

[Package BUSseq version 1.0.0 Index]