run_MNN: Run MNN to correct for platform effects

In WeiqiangZhou/SINTER: Single-cell genomic data integration

Description

This function is used run MNN to correct for platform effects between the experimental and predicted scATAC-seq data.

Usage

run_MNN(atac_data, pre_result, k, sigma, MNN_ref = "scATAC", ...)

Arguments

atac_data	scATAC-seq data for matching.
pre_result	Predicted scATAC-seq data based on scRNA-seq.
k	The number of mutual nearest neighbor in MNN.
sigma	The bandwidth of the Gaussian smoothing kernel used to compute the correction vector.
MNN_ref	A flag to determine which data type is used as reference in MNN. Select from "scATAC" and "scRNA".

Value

data_combine

The combined data matrix from all single cells.

Examples

## Not run: 
data_combine <- run_MNN(atac_data,pre_result,k=param_opt$k_opt,sigma=param_opt$sigma_opt,MNN_ref="scATAC")

## End(Not run)

WeiqiangZhou/SINTER documentation built on Sept. 11, 2019, 8:03 a.m.