From BIOlogical Sequences to MultiDimensional Scaling


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Documentation for package ‘bios2mds’ version 1.1

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bios2mds-package From BIOlogical Sequences to MultiDimensional Scaling
bios2mds From BIOlogical Sequences to MultiDimensional Scaling
col.group Links elements in a mmds object to specific groups and colors
dif Difference score
dis Dissimilarity score
extract.cluster Extraction of clusters alignments
gpcr Pre-analyzed G-Protein-Coupled Receptor (GPCR) data set
kmeans.run Multiple runs of K-means analysis
mat.dif Matrices of difference scores between sequences
mat.dis Matrices of dissimilarity scores between amino acid sequences
mmds Metric multidimensional scaling
mmds.2D.plot Plots the mmds coordinates onto a 2D space
mmds.3D.plot Plots the mmds coordinates onto a 2D space
mmds.plot Plots a summary of the mmds results
random.msa Random Alignment
read.fasta Reads a file in FASTA format
read.msf Reads a multiple sequence alignment file in MSF format
scree.plot Plots the eingenvalues of an MDS analysis
sil.score Silhouette score
sub.mat Amino acid substitution matrices
write.fasta Writes a MSA file in FASTA format
write.mmds.pdb Writes PDB file