batch_correct: Batch Correct This function allows you to Add batch corrected...

In compbiomed/BatchQC: Batch Effects Quality Control Software

Batch Correct This function allows you to Add batch corrected count matrix to the SE object

Description

Batch Correct This function allows you to Add batch corrected count matrix to the SE object

Usage

batch_correct(se, method, assay_to_normalize, batch, group = NULL,
covar, output_assay_name)

Arguments

se	SummarizedExperiment object
method	Normalization Method
assay_to_normalize	Which assay use to do normalization
batch	The batch
group	The group variable
covar	Covariate Matrix
output_assay_name	name of results assay

Value

a summarized experiment object with normalized assay appended

Examples

library(scran)
se <- mockSCE()
se <- BatchQC::batch_correct(se, method = "ComBat-Seq",
                                    assay_to_normalize = "counts",
                                    batch = "Mutation_Status",
                                    covar = "Treatment",
                                    output_assay_name =
                                        "ComBat_Seq_Corrected")
se <- BatchQC::batch_correct(se, method = "Combat",
                                    assay_to_normalize = "counts",
                                    batch = "Mutation_Status",
                                    covar = "Treatment",
                                    output_assay_name =
                                        "Combat_Corrected")
se

compbiomed/BatchQC documentation built on May 23, 2024, 6:56 a.m.