ComBatSCE: ComBatSCE

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

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)
}

mmkhan19/singleCellTK documentation built on March 22, 2022, 7:43 a.m.