corrected_read_counts {BUSseq} | R Documentation

## Generate the Corrected Read Count Matrix within the Output of the `BUSseq_MCMC`

### Description

The function generates a version of count data, for which the batch effects are removed and the biological variabilities are retained. We develop a quantile match approach based on the idea of inverse transform sampling. The users can perform downstream analysis on the corrected read count matrix, such as clustering, differentially expressed gene identification and so on, as if all the data were measured in a single batch.

### Usage

      corrected_read_counts(sce_BUSseqfit)

### Arguments

`sce_BUSseqfit` | An output `SingleCellExperiment` object obtained from the function `BUSseq_MCMC`.

### Value

`corrected_data` | The corrected read count matrix, which is added to the assays of `sce_BUSseqfit` and can be loaded by `assay(sce_BUSseqfit, "corrected_data")`.

### 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
    library(SingleCellExperiment)
    BUSseqfits_example
    BUSseqfits_corrected <- corrected_read_counts(BUSseqfits_example)
    corrected_data <- assay(BUSseqfits_corrected, "corrected_data")

[Package BUSseq version 1.0.0 Index]