Statistical Analysis Tools for High Dimension Molecular Data (HDMD)

---

Documentation for package ‘HDMD’ version 1.2

• DESCRIPTION file.

Help Pages

HDMD-package	Structural Analysis Tools for High Dimensional Molecular Data
AA54	Normalized Amino Acid Indices quantifying 54 various attributes
AAbyGroup	Amino Acid Properties
AAGroups	Amino Acid Properties
AAMetric	Amino Acid Metric Solution using R (Atchley et al 2005)
AAMetric.Atchley	Amino Acid Metric Solution (Atchley et al 2005)
AminoAcids	Amino Acid Properties
bHLH288	Alignment of basic Helix Loop Helix (bHLH) domain data
factor.pa.ginv	Principal Axis Factor Analysis when D>>N
FactorTransform	Metric Solution for Amino Acid characters
FactorTransform.default	Metric Solution for Amino Acid characters
FactorTransform.vector	Metric Solution for Amino Acid characters
HDMD	Structural Analysis Tools for High Dimensional Molecular Data
hydrophobic	Amino Acid Properties
Loadings.variation	Proportional and Cumulative Variation of Loading Components
MolecularEntropy	Molecular Entropy for DNA or Amino Acid Sequences
MolecularMI	Molecular Mutual Information
NMI	Normalized Mutual Information
pairwise.mahalanobis	Mahalanobis distances for grouped data
polar	Amino Acid Properties
Promax.only	Promax rotation (without prior Varimax rotation)
small	Amino Acid Properties