BatchRemove {MAGeCKFlute} | R Documentation

## Batch effect removal

### Description

Batch effect removal

### Usage

    BatchRemove(
      mat,
      batchMat,
      log2trans = FALSE,
      pca = TRUE,
      positive = FALSE,
      cluster = FALSE,
      outdir = NULL
    )

### Arguments

`mat` | A data frame, each row is a gene, and each column is a sample.
`batchMat` | A data frame, the first column should be 'Samples'(matched colnames of mat) and the second column is 'Batch'. The remaining columns could be Covariates.
`log2trans` | Boolean, specifying whether do logarithmic transformation before batch removal.
`pca` | Boolean, specifying whether return pca plot.
`positive` | Boolean, specifying whether all values should be positive.
`cluster` | Boolean, specifying whether perform hierarchical clustering.
`outdir` | Output directory for hierarchical cluster tree.

### Value

A list contrains two objects, including `data` and `p`.

### Author(s)

Wubing Zhang

### See Also

`ComBat`

### Examples

    edata = matrix(c(rnorm(2000, 5), rnorm(2000, 8)), 1000)
    colnames(edata) = paste0("s", 1:4)
    batchMat = data.frame(sample = colnames(edata), batch = rep(1:2, each = 2))
    edata1 = BatchRemove(edata, batchMat)
    print(edata1$p)

[Package MAGeCKFlute version 1.7.2 Index]