dot-calc_mmd_mat: Calculates mean MMD distances between all pairs of samples

In wmacnair/SampleQC: Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data

Calculates mean MMD distances between all pairs of samples

Description

Calculates mean MMD distances between all pairs of samples

Usage

.calc_mmd_mat(
  sample_list,
  mat_list,
  n_times,
  subsample,
  sigma,
  n_cores,
  bp_seed = 22
)

Arguments

sample_list	List of samples to iterate through
mat_list	List of matrices of QC metrics
n_times	How many times do we sample MMD between each pair of samples? (if subsampled, MMD is a stochastic value)
subsample	Should we downsample the number of cells per sample to this number
sigma	Scale for MMD kernel (defaults to length of qc_names)
n_cores	How many cores to parallelize over
bp_seed	random seed for BiocParallel workers

Value

matrix of MMD values

wmacnair/SampleQC documentation built on Nov. 18, 2022, 5 p.m.