ComBatSCE {singleCellTK} | R Documentation

## ComBatSCE

### Description

Run ComBat on a SCtkExperiment object

### Usage

    ComBatSCE(inSCE, batch, useAssay = "logcounts",
      par.prior = "Parametric", covariates = NULL, mean.only = FALSE,
      ref.batch = NULL)

### Arguments

`inSCE` | Input SCtkExperiment object. Required
`batch` | The name of a column in colData to use as the batch variable. Required
`useAssay` | The assay to use for ComBat. The default is "logcounts"
`par.prior` | TRUE indicates parametric adjustments will be used, FALSE indicates non-parametric adjustments will be used. Accepted parameters: "Parametric" or "Non-parametric"
`covariates` | List of other column names in colData to be added to the ComBat model as covariates
`mean.only` | If TRUE ComBat only corrects the mean of the batch effect
`ref.batch` | If given, will use the selected batch as a reference for batch adjustment.

### Value

ComBat matrix based on inputs. You can save this matrix into the SCtkExperiment with assay()

### Examples

    if(requireNamespace("bladderbatch", quietly = TRUE)) {
      library(bladderbatch)
      data(bladderdata)

      #subset for testing
      dat <- bladderEset[1:50,]
      dat <- as(as(dat, "SummarizedExperiment"), "SCtkExperiment")
      mod <- stats::model.matrix(~as.factor(cancer), data = colData(dat))

      # parametric adjustment
      combat_edata1 <- ComBatSCE(inSCE = dat, useAssay = "exprs",
                                 batch = "batch", covariates = NULL)
      assay(dat, "parametric_combat") <- combat_edata1

      # non-parametric adjustment, mean-only version
      combat_edata2 <- ComBatSCE(inSCE = dat, useAssay = "exprs",
                                 batch = "batch", par.prior = "Non-parametric",
                                 mean.only = TRUE, covariates = NULL)
      assay(dat, "nonparametric_combat_meanonly") <- combat_edata2

      # reference-batch version, with covariates
      combat_edata3 <- ComBatSCE(inSCE = dat, useAssay = "exprs",
                                 batch = "batch", covariates = "cancer",
                                 ref.batch = 3)
      assay(dat, "refbatch_combat_wcov") <- combat_edata3
      assays(dat)
    }

[Package singleCellTK version 1.2.3 Index]