runHarmony: Run harmony integration

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Run harmony integration

Description

Run harmony integration

Usage

runHarmony(
  object,
  n.dims.use = 30,
  covariates = c("data_set"),
  harmony.theta = NULL,
  harmony.lambda = NULL,
  harmony.sigma = 0.1,
  harmony.nclust = NULL,
  harmony.tau = 0,
  harmony.block.size = 0.05,
  harmony.max.iter = 10,
  harmony.max.iter.cluster = 200,
  harmony.epsilon.cluster = 1e-05,
  harmony.epsilon.harmony = 1e-04,
  n.seed = 1
)

Arguments

object	The SingCellaR object.
n.dims.use	The number of PCA dimensions used for the input for harmony.
covariates	The unwanted source of variations (e.g. batch, sample_id, etc).
harmony.theta	The harmony theta parameter. Deafult NULL. This is the diversity clustering penalty parameter. Specify for each variable in vars_use Default theta=2. theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters.
harmony.lambda	The harmony lambda parameter. Deafult NULL. Ridge regression penalty parameter. Specify for each variable in group.by.vars. Default lambda=1. Lambda must be strictly positive. Smaller values result in more aggressive correction.
harmony.sigma	The harmony sigma parameter. Default 0.1. This parameter is the width of soft kmeans clusters. Sigma scales the distance from a cell to cluster centroids. Larger values of sigma result in cells assigned to more clusters. Smaller values of sigma make soft kmeans cluster approach hard clustering.
harmony.nclust	The harmony nclust parameter. Default NULL
harmony.tau	The harmony tau parameter. Default 0. The parameter is for the protection against overclustering small datasets with large ones. tau is the expected number of cells per cluster.
harmony.block.size	The harmony block.size parameter. Default 0.05. What proportion of cells to update during clustering. Between 0 to 1. Larger values may be faster but less accurate
harmony.max.iter	The harmony max iteration parameter. Default 10. Maximum number of rounds to run Harmony. One round of Harmony involves one clustering and one correction step.
harmony.max.iter.cluster	The harmony max iteration cluster. Default 200. Maximum number of rounds to run clustering at each round of Harmony.
harmony.epsilon.cluster	The harmony epsilon.cluster parameter. Default 1e-05. Convergence tolerance for clustering round of Harmony. Set to -Inf to never stop early.
harmony.epsilon.harmony	The harmony epsilon parameter. Default 1e-04. Convergence tolerance for Harmony. Set to -Inf to never stop early.
n.seed	The set seed number.

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.