Batch Effects Correction with Unknown Subtypes

[Up] [Top]

Documentation for package ‘BUScorrect’ version 1.10.0

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