normalize_SE: This function allows you to add normalized count matrix to...

In compbiomed/BatchQC: Batch Effects Quality Control Software

This function allows you to add normalized count matrix to the SE object

Description

This function allows you to add normalized count matrix to the SE object

Usage

normalize_SE(se, method, log_bool, assay_to_normalize, output_assay_name)

Arguments

se	SummarizedExperiment Object
method	Normalization Method, either 'CPM' or 'DESeq' or 'none' for log only
log_bool	True or False; True to log normalize the data set after normalization method
assay_to_normalize	Which SE assay to do normalization on
output_assay_name	name for the resulting normalized assay

Value

the original SE object with normalized assay appended

Examples

library(scran)
se <- mockSCE()
se_CPM_normalized <- BatchQC::normalize_SE(se, method = "CPM",
                                log_bool = FALSE,
                                assay_to_normalize = "counts",
                                output_assay_name =
                                    "CPM_normalized_counts")
se_DESeq_normalized <- BatchQC::normalize_SE(se, method = "DESeq",
                                log_bool = FALSE,
                                assay_to_normalize = "counts",
                                output_assay_name =
                                    "DESeq_normalized_counts")
se_CPM_normalized
se_DESeq_normalized

compbiomed/BatchQC documentation built on April 23, 2024, 7:38 a.m.