Package: BUScorrect 1.31.0

Xiangyu Luo

BUScorrect: Batch Effects Correction with Unknown Subtypes

High-throughput experimental data are accumulating exponentially in public databases. However, mining valid scientific discoveries from these abundant resources is hampered by technical artifacts and inherent biological heterogeneity. The former are usually termed "batch effects," and the latter is often modelled by "subtypes." The R package BUScorrect fits a Bayesian hierarchical model, the Batch-effects-correction-with-Unknown-Subtypes model (BUS), to correct batch effects in the presence of unknown subtypes. BUS is capable of (a) correcting batch effects explicitly, (b) grouping samples that share similar characteristics into subtypes, (c) identifying features that distinguish subtypes, and (d) enjoying a linear-order computation complexity.

Authors:Xiangyu Luo <[email protected]>, Yingying Wei <[email protected]>

BUScorrect_1.31.0.tar.gz
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BUScorrect_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BUScorrect/json (API)

# Install 'BUScorrect' in R:

install.packages('BUScorrect', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

BUSexample_data - A simulated data set

On BioConductor:BUScorrect-1.31.0(bioc 3.24)BUScorrect-1.30.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression statisticalmethod bayesian clustering featureextraction batcheffect

4.00 score 2 scripts 16 exports 22 dependencies

Last updated from:3213fae03e. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	161
linux-devel-arm64	NOTE	230
linux-devel-x86_64	NOTE	282
source / vignettes	OK	417
linux-release-arm64	NOTE	222
linux-release-x86_64	NOTE	254
macos-release-arm64	NOTE	176
macos-release-x86_64	NOTE	380
macos-oldrel-arm64	NOTE	155
macos-oldrel-x86_64	NOTE	296
windows-devel	NOTE	197
windows-release	NOTE	218
windows-oldrel	NOTE	212
wasm-release	OK	112

Exports:adjusted_values baseline_expression_values BIC_BUS BUSgibbs calculate_EPSR_gamma calculate_EPSR_mu calculate_EPSR_sigma_sq estimate_IG_indicators IG_index location_batch_effects postprob_DE postprob_DE_thr_fun scale_batch_effects subtype_effects Subtypes visualize_data

Dependencies:abind Biobase BiocGenerics bitops caTools DelayedArray generics GenomicRanges gplots gtools IRanges KernSmooth lattice Matrix MatrixGenerics matrixStats S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment XVector

BUScorrect_user_guide

Rendered fromBUScorrect_user_guide.Rnwusingknitr::knitr

Last update: 2018-07-23
Started: 2018-06-26

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

Package: BUScorrect 1.31.0

BUScorrect: Batch Effects Correction with Unknown Subtypes

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