swamp: Visualization, analysis and adjustment of high-dimensional data in respect to sample annotations.
Version 1.2.3

The package contains 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.

Browse man pages Browse package API and functions Browse package files

AuthorMartin Lauss
Date of publication2013-03-13 14:11:11
MaintainerMartin Lauss <martin.lauss@med.lu.se>
LicenseGPL (>= 2)
Version1.2.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("swamp")

Man pages

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

Functions

adjust.linearmodel Man page
combat Man page
confounding Man page Source code
corrected.p Man page Source code
dense.plot Man page Source code
feature.assoc Man page Source code
hca.plot Man page Source code
hca.test Man page Source code
kill.pc Man page
prince Man page Source code
prince.plot Man page Source code
prince.var.plot Man page Source code
quickadjust.ref Man page Source code
quickadjust.zero Man page Source code
swamp Man page
swamp-package Man page

Files

MD5
R
R/quickadjust.zero.R
R/quickadjust.ref.R
R/prince.var.plot.R
R/prince.R
R/prince.plot.R
R/kill.pc.r
R/hca.test.R
R/hca.plot.R
R/feature.assoc.R
R/dense.plot.R
R/corrected.p.R
R/confounding.R
R/combat.R
R/adjust.linearmodel.R
NAMESPACE
man
man/swamp-package.Rd
man/quickadjust.zero.Rd
man/quickadjust.ref.Rd
man/prince.var.plot.Rd
man/prince.Rd
man/prince.plot.Rd
man/kill.pc.Rd
man/hca.test.Rd
man/hca.plot.Rd
man/feature.assoc.Rd
man/dense.plot.Rd
man/corrected.p.Rd
man/confounding.Rd
man/combat.Rd
man/adjust.linearmodel.Rd
DESCRIPTION
swamp documentation built on May 19, 2017, 10:45 p.m.