bios2mds: From BIOlogical Sequences to MultiDimensional Scaling

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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.

Author
Julien Pele with Jean-Michel Becu, Herve Abdi, and Marie Chabbert
Date of publication
2012-06-05 11:16:15
Maintainer
Marie Chabbert <marie.chabbert@univ-angers.fr>
License
GPL
Version
1.2.2

View on CRAN

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

Files in this package

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