Package: swamp 1.5.1

swamp: Visualization, Analysis and Adjustment of High-Dimensional Data in Respect to Sample Annotations

Collection of functions to connect the structure of the data with the information on the samples. Three types of associations are covered: 1. linear model of principal components. 2. hierarchical clustering analysis. 3. distribution of features-sample annotation associations. Additionally, the inter-relation between sample annotations can be analyzed. Simple methods are provided for the correction of batch effects and removal of principal components.

Authors:Martin Lauss

swamp_1.5.1.tar.gz
swamp_1.5.1.zip(r-4.7)swamp_1.5.1.zip(r-4.6)swamp_1.5.1.zip(r-4.5)
swamp_1.5.1.tgz(r-4.6-any)swamp_1.5.1.tgz(r-4.5-any)
swamp_1.5.1.tar.gz(r-4.7-any)swamp_1.5.1.tar.gz(r-4.6-any)
swamp_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
swamp/json (API)

# Install 'swamp' in R:

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

On CRAN:

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

2.42 score 1 packages 29 scripts 189 downloads 3 mentions 14 exports 8 dependencies

Last updated from:82c1ddfeb8. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	115
source / vignettes	OK	163
linux-release-x86_64	OK	116
macos-release-arm64	OK	175
macos-oldrel-arm64	OK	176
windows-devel	OK	79
windows-release	OK	71
windows-oldrel	OK	76
wasm-release	OK	89

Exports:adjust.linearmodel combat confounding corrected.p dense.plot feature.assoc hca.plot hca.test kill.pc prince prince.plot prince.var.plot quickadjust.ref quickadjust.zero

Dependencies:amap bitops caTools gplots gtools impute KernSmooth MASS

Help page	Topics
Visualization, Analysis and Adjustment of High-Dimensional Data in Respect to Sample Annotations	swamp-package swamp
Batch adjustment using a linear model	adjust.linearmodel
ComBat algorithm to combine batches.	combat
Heatmap of interrelation of sample annotations	confounding
Correction of p-values for associations between features and sample annotation	corrected.p
Density plots of feature associations in observed and permuted data	dense.plot
Associations of the features to a sample annotation in observed and reshuffled data.	feature.assoc
Dendrogram with according sample annotations	hca.plot
Tests for annotation differences among sample clusters	hca.test
Removes principal components from a data matrix	kill.pc
Linear models of prinicipal conponents dependent on sample annotations	prince
Heatmap of the associations between principal components and sample annotations	prince.plot
ScreePlot of the data variation covered by the principal components	prince.var.plot
Batch adjustment by median-scaling to a reference batch	quickadjust.ref
Batch adjustment by median-centering	quickadjust.zero

Package: swamp 1.5.1

swamp: Visualization, Analysis and Adjustment of High-Dimensional Data in Respect to Sample Annotations

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)