perform.harmony: Performs Harmony integration

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Performs Harmony integration

Description

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

Usage

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

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.