Performs Harmony integration — perform.harmony • IBRAP

Performs Harmony integration on defined method-assays and reductions contained within. This is performed on reductions.

perform.harmony(
  object,
  assay,
  batch,
  reduction = "pca",
  reduction.save.suffix = "",
  dims.use = NULL,
  print.harmony.plot = FALSE,
  seed = 1234,
  verbose = FALSE,
  ...
)

Arguments

object: IBRAP S4 class object
assay: Character. String containing indicating which assay to use
batch: Character. A string of the column nmae that contains variables to regress.
reduction: Character. String defining the name of the reduction to provide for HARMONY. Default = 'pca'
reduction.save.suffix: Character. What should be appended to the end of harmony as the reduction name
dims.use: Numerical. Number of dimensions of the provided reduction to input into harmony, NULL equates to all dimensions. Default = NULL
print.harmony.plot: Boolean. Should the automatically generated plot be printed? Default = FALSE

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seed: Numeric. What should the seed be set as. Default = 1234

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verbose: Logical Should function messages be printed?
...: Arguments to be passed to harmony::HarmonyMatrix

Value

PCA reductions contained within the computational_reduction list in the defined assays

Examples


object <- perform.harmony(object = object, 
                          assay = c('SCRAN', 'SCT', 'SCANPY'), 
                          batch = 'original.project', 
                          reduction = c('pca'),  
                          max.iter.harmony = 100,
                          dims.use = list(NULL))
#> Error in is(object = object, class2 = "IBRAP"): object 'object' not found