High Dimensional Molecular Data (HDMD) typically have many more variables or dimensions than observations or replicates (D>>N). This can cause many statistical procedures to fail, become intractable, or produce misleading results. This package provides several tools to reduce dimensionality and analyze biological data for meaningful interpretation of results. Factor Analysis (FA), Principal Components Analysis (PCA) and Discriminant Analysis (DA) are frequently used multivariate techniques. However, PCA methods prcomp and princomp do not reflect the proportion of total variation of each principal component. Loadings.variation displays the relative and cumulative contribution of variation for each component by accounting for all variability in data. When D>>N, the maximum likelihood method cannot be applied in FA and the the principal axes method must be used instead, as in factor.pa of the psych package. The factor.pa.ginv function in this package further allows for a singular covariance matrix by applying a general inverse method to estimate factor scores. Moreover, factor.pa.ginv removes and warns of any variables that are constant, which would otherwise create an invalid covariance matrix. Promax.only further allows users to define rotation parameters during factor estimation. Similar to the Euclidean distance, the Mahalanobis distance estimates the relationship among groups. pairwise.mahalanobis computes all such pairwise Mahalanobis distances among groups and is useful for quantifying the separation of groups in DA. Genetic sequences are composed of discrete alphabetic characters, which makes estimates of variability difficult. MolecularEntropy and MolecularMI calculate the entropy and mutual information to estimate variability and covariability, respectively, of DNA or Amino Acid sequences. Functional grouping of amino acids (Atchley et al 1999) is also available for entropy and mutual information estimation. Mutual information values can be normalized by NMI to account for the background distribution arising from the stochastic pairing of independent, random sites. Alternatively, discrete alphabetic sequences can be transformed into biologically informative metrics to be used in various multivariate procedures. FactorTransform converts amino acid sequences using the amino acid indices determined by Atchley et al 2005.
Author  Lisa McFerrin 
Date of publication  20130227 07:31:03 
Maintainer  Lisa McFerrin <lgmcferr@ncsu.edu> 
License  GPL (>= 2) 
Version  1.2 
Package repository  View on CRAN 
Installation  Install the latest version of this package by entering the following in R:



All man pages Function index File listing
Man pages  

AA54: Normalized Amino Acid Indices quantifying 54 various...  
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  
HDMDpackage: Structural Analysis Tools for High Dimensional Molecular Data  
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  
Promax.only: Promax rotation (without prior Varimax rotation) 
Functions  

AA54  Man page 
AAGroups  Man page 
AAMetric  Man page 
AAMetric.Atchley  Man page 
AAbyGroup  Man page 
AminoAcids  Man page 
FactorTransform  Man page Source code 
FactorTransform.default  Man page Source code 
FactorTransform.vector  Man page Source code 
HDMD  Man page 
HDMDpackage  Man page 
Loadings.variation  Man page Source code 
MolecularEntropy  Man page Source code 
MolecularMI  Man page Source code 
NMI  Man page Source code 
Promax.only  Man page Source code 
bHLH288  Man page 
factor.pa.ginv  Man page Source code 
hydrophobic  Man page 
pairwise.mahalanobis  Man page Source code 
polar  Man page 
small  Man page 
Files  

MD5
 
R
 
R/HDMD_package.R  
R/bHLH288.R  
R/AA54.R  
NAMESPACE
 
man
 
man/Promax.only.Rd  
man/pairwise.mahalanobis.Rd  
man/NMI.Rd  
man/MolecularMI.Rd  
man/MolecularEntropy.Rd  
man/Loadings.variation.Rd  
man/HDMDpackage.Rd  
man/FactorTransform.Rd  
man/factor.pa.ginv.Rd  
man/bHLH288.Rd  
man/AminoAcids.Rd  
man/AAMetric.Rd  
man/AAMetric.Atchley.Rd  
man/AA54.Rd  
DESCRIPTION

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