corrected_read_counts {BUSseq} | R Documentation |
BUSseq_MCMC
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.
corrected_read_counts(sce_BUSseqfit)
sce_BUSseqfit |
An output |
corrected_data |
The corrected read count matrix, which is added to
the assays of |
Fangda Song
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.
# "BUSseqfits_example" is an example output library(SingleCellExperiment) BUSseqfits_example BUSseqfits_corrected <- corrected_read_counts(BUSseqfits_example) corrected_data <- assay(BUSseqfits_corrected, "corrected_data")