# Batch Effects Correction with Unknown Subtypes

## Documentation for package ‘BUScorrect’ version 1.31.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

BUScorrect-package | Batch Effects Correction with Unknown Subtypes
adjusted_values | Obtain adjusted expression values from the output by BUSgibbs
baseline_expression_values | Obtain the baseline expression values from the output by BUSgibbs
BIC_BUS | Obtain BIC form the output by BUSgibbs
BUScorrect | Batch Effects Correction with Unknown Subtypes
BUSexample_data | A simulated data set
BUSgibbs | Batch Effects Correction and Subtype Discovery using Gibbs Sampler
calculate_EPSR_gamma | Calculate the estimated potential scale reduction factors (EPSR factors) for location batch effects
calculate_EPSR_mu | Calculate the estimated potential scale reduction factors (EPSR factors) for subtype effects
calculate_EPSR_sigma_sq | Calculate the estimated potential scale reduction factors (EPSR factors) for the variances of expression values
estimate_IG_indicators | Estimate the intrinsic gene indicators
IG_index | Obtain the intrinsic gene indices
location_batch_effects | Obtain the location batch effects from the output by BUSgibbs
postprob_DE | Calculate the posterior probability of being differentially expressed
postprob_DE_thr_fun | Select the the posterior probability threshold to control the false discovery rate
print.BUSfits | Print the output by BUSgibbs
scale_batch_effects | Obtain the scale batch effects from the output by 'BUSgibbs'
Subtypes | Obtain the subtype indicators from the output by 'BUSgibbs'
subtype_effects | Obtain the subtype effects from the output by 'BUSgibbs'
summary.BUSfits | Summary the output by 'BUSgibbs'
visualize_data | Visualize the gene expression data from multiple batches