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

Documentation for package ‘swamp’ version 1.3.1

swamp-package	Visualization, analysis and adjustment of high-dimensional data in respect to sample annotations.
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 sample annotation
dense.plot	Density plots of feature associations in observed and permuted data
feature.assoc	Associations of the features to a sample annotation in observed and reshuffled data.
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 annotations
prince.plot	Heatmap of the associations between principal components and sample annotations
prince.var.plot	ScreePlot of the data variation covered by the principal components
quickadjust.ref	Batch adjustment by median-scaling to a reference batch
quickadjust.zero	Batch adjustment by median-centering
swamp	Visualization, analysis and adjustment of high-dimensional data in respect to sample annotations.