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bios2mds (version 1.2.2)

From BIOlogical Sequences to MultiDimensional Scaling

Description

Bios2mds is primarily dedicated to the analysis of biological sequences by metric MultiDimensional Scaling with projection of supplementary data. It contains functions for reading multiple sequence alignment files, calculating distance matrices, performing metric multidimensional scaling and visualizing results.

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Version

Install

install.packages('bios2mds')

Monthly Downloads

390

Version

1.2.2

License

GPL

Maintainer

Marie Chabbert

Last Published

June 5th, 2012

Functions in bios2mds (1.2.2)

mat.dif

Matrices of difference scores between sequences
mmds.project

Metric multidimensional Scaling Projection
mmds.3D.plot

Display the mmds coordinates onto a 3D space
dis

Dissimilarity score
import.fasta

Reads a file in FASTA format
bios2mds-package

From BIOlogical Sequences to MultiDimensional Scaling
mmds

Metric multidimensional scaling
dif

Difference score
mmds.2D.plot

Plots the mmds coordinates onto a 2D space
export.fasta

Writes a MSA file in FASTA format
extract.cluster

Extraction of clusters alignments
mmds.2D.multi

Plots the mmds coordinates onto a 2D space
sub.mat

Amino acid substitution matrices
import.msf

Reads a multiple sequence alignment file in MSF format
gpcr

Pre-analyzed G-Protein-Coupled Receptor (GPCR) data set
mmds.plot

Plots a summary of the mmds results
random.msa

Random Alignment
sil.score

Silhouette score
scree.plot

Plots the eingenvalues of an MDS analysis
write.mmds.pdb

Writes PDB file
col.group

Links elements in a mmds object to specific groups and colors
kmeans.run

Multiple runs of K-means analysis
mat.dis

Matrices of dissimilarity scores between amino acid sequences