scBatch: Correct scRNA-seq count matrix subject to batch effects by...

In tengfei-emory/scBatch: Batch Effect Correction Through Sample Distance Matrix Correction

Description

As an extension of package 'QuantNorm', which corrects the distance matrix to obtain reasonable sample pattern, this package use gradient descent algorithm to correct count matrix by linear transformation.

Usage

scBatch(
  count.mat,
  dist.mat,
  weight.mat,
  m,
  max.iter = 30,
  step.size = 1e-04,
  tol = 1e-10
)

Arguments

count.mat	The original p*n batch effect data with n subjects and p RNA-seq measurements.
dist.mat	The n*n distance matrix obtained by QuantNorm.
weight.mat	An initial n*n weight matrix to conduct linear transformation. Default to be identity matrix if not specified.
m	Number of groups to be divided for coordinate gradient descent. 1 < m <= n. Default to be 0.1n if not specified.
max.iter	Maximum number of the iteration if the tolerance is not reached.
step.size	Step size of the gradient descent algorithm.
tol	Stopping criteria of the algorithm. The algorithm stops if the step size is smaller than tol.

Value

Returns the corrected count matrix.

Author(s)

Teng Fei. Email: [e-mail]

References

Fei and Yu (2020). scBatch: batch-effect correction of RNA-seq data through sample distance matrix adjustment. Bioinformatics, 36(10), 3115-3123. <https://doi.org/10.1093/bioinformatics/btaa097>

tengfei-emory/scBatch documentation built on June 6, 2021, 10:22 p.m.