bios2mds: From BIOlogical Sequences to MultiDimensional Scaling
Version 1.2.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorJulien Pele with Jean-Michel Becu, Herve Abdi, and Marie Chabbert
Date of publication2012-06-05 11:16:15
MaintainerMarie Chabbert <marie.chabbert@univ-angers.fr>
LicenseGPL
Version1.2.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bios2mds")

Man pages

bios2mds-package: 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
export.fasta: Writes a MSA file in FASTA format
extract.cluster: Extraction of clusters alignments
gpcr: Pre-analyzed G-Protein-Coupled Receptor (GPCR) data set
import.fasta: Reads a file in FASTA format
import.msf: Reads a multiple sequence alignment file in MSF format
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.multi: Plots the mmds coordinates onto a 2D space
mmds.2D.plot: Plots the mmds coordinates onto a 2D space
mmds.3D.plot: Display the mmds coordinates onto a 3D space
mmds.plot: Plots a summary of the mmds results
mmds.project: Metric multidimensional Scaling Projection
random.msa: Random Alignment
scree.plot: Plots the eingenvalues of an MDS analysis
sil.score: Silhouette score
sub.mat: Amino acid substitution matrices
write.mmds.pdb: Writes PDB file

Functions

bios2mds Man page
bios2mds-package Man page
col.group Man page Source code
dif Man page Source code
dis Man page Source code
export.fasta Man page Source code
extract.cluster Man page Source code
gpcr Man page
import.fasta Man page Source code
import.msf Man page Source code
is.aa Source code
is.gap Source code
kmeans.run Man page Source code
mat.dif Man page Source code
mat.dis Man page Source code
mmds Man page Source code
mmds.2D.multi Man page Source code
mmds.2D.plot Man page Source code
mmds.3D.plot Man page Source code
mmds.plot Man page Source code
mmds.project Man page Source code
random.msa Man page Source code
scree.plot Man page Source code
sil.score Man page Source code
sub.mat Man page
write.mmds.pdb Man page Source code

Files

MD5
data
data/gpcr.rda
data/datalist
data/sub.mat.rda
man
man/gpcr.Rd
man/col.group.Rd
man/scree.plot.Rd
man/random.msa.Rd
man/write.mmds.pdb.Rd
man/mat.dis.Rd
man/mmds.project.Rd
man/mmds.2D.plot.Rd
man/import.fasta.Rd
man/dis.Rd
man/export.fasta.Rd
man/mat.dif.Rd
man/dif.Rd
man/sub.mat.Rd
man/mmds.2D.multi.Rd
man/extract.cluster.Rd
man/bios2mds-package.Rd
man/mmds.3D.plot.Rd
man/mmds.Rd
man/kmeans.run.Rd
man/import.msf.Rd
man/sil.score.Rd
man/mmds.plot.Rd
inst
inst/doc
inst/doc/bios2mds.pdf
inst/csv
inst/csv/human_gpcr_group.csv
inst/csv/drome_gpcr_group.csv
inst/msa
inst/msa/human_gpcr.msf
inst/msa/drome_gpcr.fa
inst/msa/human_gpcr.fa
inst/msa/drome_gpcr.msf
NAMESPACE
R
R/mmds.2D.multi.R
R/dis.R
R/kmeans.run.R
R/mat.dis.R
R/mmds.2D.plot.R
R/import.fasta.R
R/is.gap.R
R/extract.cluster.R
R/mmds.R
R/dif.R
R/mmds.3D.plot.R
R/col.group.R
R/mmds.project.R
R/sil.score.R
R/random.msa.R
R/import.msf.R
R/mat.dif.R
R/is.aa.R
R/write.mmds.pdb.R
R/scree.plot.R
R/mmds.plot.R
R/export.fasta.R
DESCRIPTION
ChangeLog
bios2mds documentation built on May 19, 2017, 11:35 p.m.