EkfBE: Correction vector estimation

In Canek: Batch Correction of Single Cell Transcriptome Data

Correction vector estimation

Description

Batch effect estimation using an extended Kalman filter

Usage

EkfBE(
  refBatch,
  queBatch,
  pairs,
  sampling = FALSE,
  numSamples = NULL,
  verbose = FALSE
)

Arguments

refBatch	Reference batch.
queBatch	Query batch.
pairs	A numerical matrix containing MNNs pairs cell indexes. First column corresponds to query batch cells.
sampling	Sample MNNs pairs.
numSamples	If sampling, number of MNNs pairs samples to use on the estimation process.
verbose	Print output.

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, causing a linear deviation between the reference and the query batches.

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.

Canek documentation built on Nov. 6, 2023, 1:06 a.m.