Amino Acid Metric Solution using R (Atchley et al 2005)

Description

Atchley et al 2005 performed factor analysis on a set of Amino Acid Indices (AA54) and inferred a 5 factor latent variable structure relating amino acid characteristics using SAS. An equivalent analysis was performed using factor.pa.ginv from the HDMD package in R. Based on the relationship between factors and variable descriptions, the latent variables are defined as Factor1 (PAH): Polarity, Accessibility, Hydrophobicity; Factor2 (PSS): Propensity for Secondary Structure; Factor3 (MS) : Molecular Size; Factor4 (CC): Codon Composition; Factor5 (EC): Electrostatic Charge. While the Factor Analysis loadings were the same, R and SAS calculated scores slightly differently. AAMetric are scores from the R factor analysis which convey the similarities and differences among amino acids (rows) for each latent variable (columns).

Format

Rows are alphabetized Amino Acids and the 5 columns are factors where Factor1 (PAH): Polarity, Accessibility, Hydrophobicity; Factor2 (PSS): Propensity for Secondary Structure; Factor3 (MS) : Molecular Size; Factor4 (CC): Codon Composition; Factor5 (EC): Electrostatic Charge.

Details

54 Amino Acid Indices were selected from www.genome.jp/aaindex to quantify Amino Acid Similarities. Using Factor Analysis on 5 factors, interpretable latent variables were determined to quantify Amino Acid attributes. These are the scores from factor analysis calculated by factor.pa.ginv in R.

Source

Method similar to Atchley, W. R., Zhao, J., Fernandes, A. and Drueke, T. 2005. Solving the sequence "metric" problem: Proc. Natl. Acad. Sci. USA 102: 6395-6400.

See Also

AAMetric.Atchley, factor.pa.ginv

Examples

data(AAMetric)
 plot(AAMetric[,1], AAMetric[,2], pch = AminoAcids) 
 
 cor(AAMetric, AAMetric.Atchley)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(HDMD)
Loading required package: psych
Loading required package: MASS
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HDMD/AAMetric.Rd_%03d_medium.png", width=480, height=480)
> ### Name: AAMetric
> ### Title: Amino Acid Metric Solution using R (Atchley et al 2005)
> ### Aliases: AAMetric
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AAMetric)
Warning message:
In data(AAMetric) : data set 'AAMetric' not found
>  plot(AAMetric[,1], AAMetric[,2], pch = AminoAcids) 
>  
>  cor(AAMetric, AAMetric.Atchley)
            pah           pss          ms          cc          ec
pah  0.99530421  0.0736871113 -0.12587574 -0.11889767  0.03117132
pss  0.05875309  0.9826834483 -0.08629297  0.06208317  0.04304136
ms  -0.31217404 -0.2978205891  0.37953125 -0.26553117  0.20126148
cc  -0.16603923  0.0340235286 -0.16418210  0.98779448 -0.12086778
ec  -0.04245232 -0.0001209467 -0.27474905  0.09063324 -0.66015554
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>