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

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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.

Author
Martin Lauss
Date of publication
2013-03-13 14:11:11
Maintainer
Martin Lauss <martin.lauss@med.lu.se>
License
GPL (>= 2)
Version
1.2.3

View on CRAN

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...

Files in this package

swamp
swamp/MD5
swamp/R
swamp/R/quickadjust.zero.R
swamp/R/quickadjust.ref.R
swamp/R/prince.var.plot.R
swamp/R/prince.R
swamp/R/prince.plot.R
swamp/R/kill.pc.r
swamp/R/hca.test.R
swamp/R/hca.plot.R
swamp/R/feature.assoc.R
swamp/R/dense.plot.R
swamp/R/corrected.p.R
swamp/R/confounding.R
swamp/R/combat.R
swamp/R/adjust.linearmodel.R
swamp/NAMESPACE
swamp/man
swamp/man/swamp-package.Rd
swamp/man/quickadjust.zero.Rd
swamp/man/quickadjust.ref.Rd
swamp/man/prince.var.plot.Rd
swamp/man/prince.Rd
swamp/man/prince.plot.Rd
swamp/man/kill.pc.Rd
swamp/man/hca.test.Rd
swamp/man/hca.plot.Rd
swamp/man/feature.assoc.Rd
swamp/man/dense.plot.Rd
swamp/man/corrected.p.Rd
swamp/man/confounding.Rd
swamp/man/combat.Rd
swamp/man/adjust.linearmodel.Rd
swamp/DESCRIPTION