From Biological Sequences and Simulations to Correlation Analysis

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Documentation for package ‘Bios2cor’ version 1.2

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bios2cor-package Correlation Analysis in Biological Sequences and Simulations
angle_conversion Conversion of dihedral angles to rotamers
ang_evo_graph Angle evolution graphs
Bios2cor Correlation Analysis in Biological Sequences and Simulations
bios2cor Correlation Analysis in Biological Sequences and Simulations
centered_pca Principal component analysis of a correlation/covariation matrix
corr_contact Calculates the number of contacts for each element of the top pairs
create_boxplot Creates boxplot file
create_corrfile Creates a correlation file
create_entropyfile Stores entropy values
create_network Creates network structure of top elements
create_pcafile Creates a file of coordinates in PCA space
create_screeplot Creates PCA screeplot
cyto_entropy Creation of a entropy file in Cytoscape format
cyto_zscore Creation of a Z-score file in Cytoscape format
delta_weighting Creation of a Delta weighting filter for each element
dynamic_struct Creates the data structure for the analysis of side chain dihedral angles
elsc ELSC(Explicit Likelihood of Subset Covariation) function
entropy Entropy score
entropy_graph Entropy graph
gauss_weighting Creation of a gaussian weighting filter for each element
import.fasta Reads a file in FASTA format
import.msf Reads a multiple sequence alignment file in MSF format
mcbasc McBASC(McLachlan Based Substitution Correlation) function
mip MIp(Mutual Information product) function
omes OMES(Observed minus Expected Squared) function
pca_2d PCA projection on two dimensions
random.msa Random Alignment
rotamer_circular Circular correlation
rotamer_entropy Entropy score
rotamer_mip MIP(Mutual Information Product) function applied to rotamers in molecular dynamics simulations
rotamer_omes OMES(Observed minus Expected Squared) function applied to rotamers in molecular dynamics simulations
shuffle_all Amino acids shuffle
shuffle_positions Amino acids shuffle
sigmoid_weighting Sigmoid weighting for each position
write_pdb PDB and PML file creation for 3D representation of PCA analysis
xyz2torsion Convert Cartesian Coordinates to Torsion Angles