batchComBat: Batch correct data using ComBat
In farrellja/URD: URD

Batch correct data using ComBat

batchComBat(
  object,
  batch.column,
  adjustment.columns = NULL,
  reference.batch = NULL,
  genes.correct = NULL,
  thresh.out = 0.05,
  min.out = 0,
  max.out = (ceiling(max(object@logupx.data)) + 1),
  parametric.prior = T,
  prior.plots = F,
  verbose = F
)

`object`	An URD object
`batch.column`	(Character) Name of column in `@meta` that encodes batch information.
`adjustment.columns`	(Character vector) Name of columns in `@meta` that encode information to make sure not to correct (e.g. developmental stage, etc.)
`reference.batch`	(Character) Name of reference batch to hold constant (default `NULL` adjusts all batches toward each other)
`genes.correct`	(Character vector) Which genes to correct (default `NULL` corrects all genes)
`thresh.out`	(Numeric) To keep matrix sparse, change values less than this to `min.out`
`min.out`	(Numeric) Minimum gene expression value to return
`max.out`	(Numeric) Maximum gene expression value to return (Default: capped at maximum gene expression value of original data + 1.)
`parametric.prior`	(Logical) ComBat option: Assume normal distributed gene expression (Warning: extremely slow if FALSE)
`prior.plots`	(Logical) ComBat option: Plots to compare empirical and parametric batch (see `ComBat` for more info.)
`verbose`	(Logical) Print progress