integrate_harmony: Integrate a list of SingleCellExperiment (SCE) objects using...

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

Integrate a list of SingleCellExperiment (SCE) objects using the harmony approach from the 'harmony' package. Source: https://cran.r-project.org/web/packages/harmony/index.html

Description

Integrate a list of SingleCellExperiment (SCE) objects using the harmony approach from the 'harmony' package. Source: https://cran.r-project.org/web/packages/harmony/index.html

Usage

integrate_harmony(
  merged_sce,
  batch_column,
  covariate_cols = c(),
  batch_lambda = 1,
  covariate_lambda = c(),
  ...
)

Arguments

merged_sce	A merged SCE object as prepared by 'scpcaTools::merge_sce_list()'.
batch_column	The column in the merged SCE object indicating batches being integrated.
covariate_cols	A vector of other columns to consider as covariates during integration.
batch_lambda	The ridge regression penalty to use when correcting using the 'batch_column'. Default is 1.
covariate_lambda	A vector of ridge regression penalties to use with each covariate. A lambda value must be provided for each covariate column.
...	Additional arguments to pass into 'harmony::RunHarmony()'

Value

Integrated PCs as calculated by 'harmony'

AlexsLemonade/scpcaTools documentation built on July 12, 2024, 8:34 a.m.