SnapATAC_runHarmony: Perform batch effect using harmony

In beyondpie/smmtools: Single-cell multi-omics sequenceing data tools

Perform batch effect using harmony

Description

Perform batch effect using harmony

Usage

SnapATAC_runHarmony(
  mapSnapATAC,
  meta_data,
  nPC = 30,
  vars_use = NULL,
  weightDimReduct = FALSE
)

Arguments

mapSnapATAC	list, output of SnapATAC_runDiffusionMaps, at least contains dmat matrix, cell by feature, dense matrix of embedding for the cells sdev numeric vector, standard deviation from runDiffusionMaps.
meta_data	Either (1) Dataframe with variables to integrate or (2) vector with labels.
nPC	integer, how many PCs used for Harmony, default is 30.
vars_use	string, if meta_data is dataframe, this defined which variable(s) to remove (character vector). Default is NULL
weightDimReduct	bool, if weighted the PCs by multiplying sdev, default is FALSE

Value

Matrix, cell by updated principle components

beyondpie/smmtools documentation built on July 1, 2022, 4:33 a.m.