perform.scanorama: Performs Scanorama integration

In connorhknight/IBRAP_no_decontX: Integrated Benchmarking scRNA-seq Analytical Pipeline

Description

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

Usage

perform.scanorama(
  object,
  assay,
  slot = "norm.scaled",
  split.by,
  n.dims = 50,
  reduction.save.suffix = "",
  batch_size = 5000,
  approx = TRUE,
  sigma = 15,
  alpha = 0.1,
  knn = 20,
  union = FALSE,
  seed = 12345
)

Arguments

object	IBRAP S4 class object
assay	Character. String containing indicating which assay to use
slot	Character. String defining which slot in the assay to supply to Scanorama. Default = NULL
split.by	Character. indicating the metadata column containing the batch to split the assay by.
n.dims	Numerical. The number of Scanorama dimensions to be produced. Default = 50
reduction.save.suffix	Character. Should a suffix be added to the end of scanorama, This cannot include underscores.
batch_size	Numerical. The batch size used in the alignment vector computation. Useful when integrating large datasets. Default = 5000
approx	Boolean. Use appoximate nearest neighbours within python, speeds up runtime. Default = TRUE
sigma	Numerical. Correction smoothing parameter on Gaussian kernel. Default = 15
alpha	Numerical. Alignment score minimum cutoff. Default = 0.1
knn	Numerical. Number of nearest neighbors to use for matching. Default = 20
union	Boolean. Should genes between datasets be intersected or not. Default = FALSE
seed	Numerical. The seed to use when integrating these datasets. Default = 12345

Value

Scanorama reduction saved in the supplied method-assays

Examples

object <- perform.scanorama(object = object, 
                            assay = c('SCT', 'SCRAN', 'SCANPY'), 
                            slot = 'norm.scaled', 
                            split.by = 'original.project', 
                            n.dims = 50)

connorhknight/IBRAP_no_decontX documentation built on Feb. 13, 2022, 2:32 p.m.