batchCorrectionAssay: Remove batch effects from (count/intensity) values of a...

In tnaake/MatrixQCvis: Shiny-based interactive data-quality exploration for omics data

Remove batch effects from (count/intensity) values of a SummarizedExperiment

Description

The function batchCorrectionAssay removes the batch effect of (count/intensity) values of a SummarizedExperiment. It uses either the removeBatchEffect or ComBat functions or no batch effect correction method (pass-through, none).

Usage

batchCorrectionAssay(
  se,
  method = c("none", "removeBatchEffect (limma)", "ComBat"),
  batch = NULL,
  batch2 = NULL,
  ...
)

Arguments

se	SummarizedExperiment
method	character, one of "none" or "removeBatchEffect"
batch	character, NULL or one of colnames(colData(se))
batch2	character, NULL or one of colnames(colData(se))
...	further arguments passed to removeBatchEffect or ComBat

Details

The column batch in colData(se) contains the information on the batch identity. For method = "removeBatchEffect (limma)", batch2 may indicate a second series of batches. Internal use in shinyQC.

If batch is NULL and method is set to method = "removeBatchEffect (limma)" or method = "ComBat", no batch correction will be performed (equivalent to method = "none").

The method ComBat will only perform batch correction on valid features: (1) more or equal than two observations (no NA) per level and per feature, (2) variance greater than 0 per feature, and (3) more than two valid features as given by (1) and (2). For non-valid features, values are taken from assay(se).

Value

matrix

Examples

## create se
a <- matrix(seq_len(100), nrow = 10, ncol = 10, 
    dimnames = list(seq_len(10), paste("sample", seq_len(10))))
a[c(1, 5, 8), seq_len(5)] <- NA
set.seed(1)
a <- a + rnorm(100)
cD <- data.frame(name = colnames(a), 
    type = c(rep("1", 5), rep("2", 5)), batch = rep(c(1, 2), 5))
rD <- data.frame(spectra = rownames(a))
se <- SummarizedExperiment::SummarizedExperiment(assay = a, 
    rowData = rD, colData = cD)

## method = "removeBatchEffect (limma)"
batchCorrectionAssay(se, method = "removeBatchEffect (limma)", 
    batch = "batch", batch2 = NULL)

## method = "ComBat"
batchCorrectionAssay(se, method = "ComBat", 
    batch = "batch", batch2 = NULL)

tnaake/MatrixQCvis documentation built on Nov. 4, 2024, 7:42 a.m.