EkfBE {Canek} | R Documentation |
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.
[Package Canek version 0.2.5 Index]