View source: R/benchmark.intergation.R
benchmark.integration | R Documentation |
Adopting scones method of Average Silhouette Width determination between batches. A depleted value is superior.
benchmark.integration( object, batch, assays, reduction, result.names, n.components = 2, threads = 1 )
object |
IBRAP S4 class object |
batch |
Character. Whcih column in the metadata dataframe contains the batches. |
reduction |
Character. Which reduction(s) should be used to observe integration. |
result.names |
Character. A vector of names for the benchmarking results. |
n.components |
Numerical. How many components of the reduced embeddings should be used. Default = 2 |
assay |
Character. String containing indicating which assay to use |
Benchmarking scores for the supplied integrations
object <- benchmark.integration(object = object, batch = 'original.project', assays = c('SCT','SCRAN','SCANPY'), reduction = c('pca_umap', 'pca_harmony_umap', 'scanorama_umap', 'pca_bbknn_bbknn:umap', 'CCA_pca_umap'), result.names = c('uncorrected', 'harmony', 'scanorama', 'bbknn', 'cca'), n.components = 2)
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