MeanBE {Canek}

MeanBE

Description

Batch effect estimation using the MNNs pairs.

Usage

MeanBE(refBatch, queBatch, pairs)

Arguments

refBatch

Reference batch.

queBatch

Query batch.

pairs

A numerical matrix containing MNNs pairs cell indexes. First column corresponds to query batch cells.

Details

The input batches must have the same number of genes. The model used on the estimation has the form of g_ref = g_que + be, where the batch effect is represented as a value added to the reference gene expression. The batch effect is estimated as the median of the gene expression difference among the reference and the query batch, e.g. Median(g_ref - g_que).

Value

A list containing the estimated correction vector and the estimation data. The length of the correction vector is equal to the number of genes.