Amino Acid Substitution Effect Analyser


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Documentation for package ‘aaSEA’ version 1.1.0

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AAindex A data frame of 533 amino acid properties from AAindex.
corSubFile A data frame of correlated sites.
Cruciani A data frame of 3 Cruciani properties for 20 amino acids.
Fasgai A data frame of six Fasgai vectors for 20 amino acids.
getAASub Get amino acid substitutions from multiple sequence alignment
getCorPropChange Get property changes associated with correlated substitutions
getCorSites Get correlated sites with substitutions
getPropChange Get wild type and substituted amino acid properties and associated property changes
getPropCorr Get amino acid property wise correlations of co-evolving columns of a multiple sequence alignment
getTopSub Get sites with more than one-correlated substitutions other than conserved amino acids at that position
Kidera A data frame of 10 Kidera factors for 20 amino acids
matEncode Function to encode Correlated columns of alignment matrix with desired properties
plotCorNet simple interactive network diagram of correlated substitution pairs
plotCorSubChanges Plot co-evolving sites with selected property correlations
plotMultiSubChange Plots heat map of multiple substitution associated changes per site
plotSingleSubChange Plots single substitution change histogram
startSeaShiny Title Enables to start and run the app