Learn more about Bioinformatics Toolbox

Function Reference

Alphabetical List  Class Reference

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Constructor Create objects Data Formats and Databases Read data into MATLAB software from Web databases; read and write to files using specific sequence data formats Data Visualization Plot and visualize data Trace Tools Read data from SCF file and draw nucleotide trace plots Sequence Conversion Convert nucleotide and amino acid sequences between character and integer formats, reverse and complement order of nucleotide bases, and translate nucleotides codons to amino acids Sequence Utilities Calculate consensus sequence from set of multiply aligned sequences, run BLAST search from MATLAB environment, search sequences using regular expressions, and return information about sequence file Sequence Statistics Determine base counts, nucleotide density, codon bias, and CpG islands; search for words and identify open reading frames (ORFs) Sequence Visualization Visualize sequence data Pairwise Sequence Alignment Compare nucleotide or amino acid sequences using pairwise sequence alignment functions Multiple Sequence Alignment Compare sets of nucleotide or amino acid sequences; progressively align sequences using phylogenetic tree for guidance Scoring Matrices Standard scoring matrices such as PAM and BLOSUM families of matrices that alignment functions use Phylogenetic Tree Tools Read phylogenetic tree files, calculate pairwise distances between sequences, and build a phylogenetic tree Phylogenetic Tree Methods Select, modify, and plot phylogenetic trees using phytree object methods Graph Theory Apply basic graph theory algorithms to sparse matrices Graph Visualization Methods View relationships between data visually with interactive maps, hierarchy plots, and pathways using biograph object methods Gene Ontology Read Gene Ontology formatted files Gene Ontology Methods Explore and analyze Gene Ontology data using geneont object methods Protein Analysis Determine protein characteristics and simulate enzyme cleavage reactions Profile Hidden Markov Models Get profile hidden Markov model data from the PFAM database or create your own profiles from set of sequences Microarray File Formats Read data from common microarray file formats including Affymetrix GeneChip, ImaGene results, and SPOT files; read GenePix GPR and GAL files Microarray Utilities Using Affymetrix and GeneChip data sets, get library information for probe, gene information from probe set, and probe set values from CEL and CDF information; show probe set information from NetAffx Web site and plot probe set values Microarray Data Analysis and Visualization Analyze and visualize microarray data with t-tests, spatial plots, box plots, loglog plots, and intensity-ratio plots Microarray Normalization and Filtering Normalize microarray data with lowess and mean normalization functions; filter raw data for cleanup before analysis BioIndexedFile Methods Access and read data from source file associated with BioIndexedFile object BioRead Methods Explore and analyze sequence quality data using BioRead object methods BioMap Methods Explore and analyze sequence alignment and mapping data using BioMap object methods HeatMap Methods Visualize and explore heat maps using HeatMap object methods Clustergram Methods Visualize and explore hierarchical clustering analysis data using clustergram object methods ExpressionSet Methods Explore and analyze microarray data using ExpressionSet object methods ExptData Methods Explore and analyze microarray data using ExptData object methods DataMatrix Methods Explore and analyze microarray data using DataMatrix object methods MetaData Methods Explore and analyze microarray data using MetaData object methods MIAME Methods Explore and analyze microarray data using MIAME object methods Statistical Learning Classify and identify features in data sets, set up cross-validation experiments, and compare different classification methods Mass Spectrometry Read data from common mass spectrometry file formats, preprocess raw mass spectrometry data from instruments, and analyze spectra to identify patterns and compounds Bioanalytics Read, process, and analyze data from any separation technique that produces signal data, such as spectroscopy, NMR, electrophoresis, or chromatography

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Constructor

biograph	Create biograph object
clustergram	Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
DataMatrix	Create DataMatrix object
geneont	Create geneont object and term objects
HeatMap	Display heat map of matrix data and create HeatMap object
phytree	Create phytree object

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Data Formats and Databases

affyprobeseqread	Read data file containing probe sequence information for Affymetrix GeneChip array
affyread	Read microarray data from Affymetrix GeneChip file
affysnpannotread	Read Affymetrix Mapping DNA array data from CSV-format annotation file
agferead	Read Agilent Feature Extraction Software file
blastformat	Create local BLAST database
blastread	Read data from NCBI BLAST report file
blastreadlocal	Read data from local BLAST report
celintensityread	Read probe intensities from Affymetrix CEL files
cytobandread	Read cytogenetic banding information
emblread	Read data from EMBL file
fastainfo	Return information about FASTA file
fastaread	Read data from FASTA file
fastawrite	Write to file using FASTA format
fastqinfo	Return information about FASTQ file
fastqread	Read data from FASTQ file
fastqwrite	Write to file using FASTQ format
galread	Read microarray data from GenePix array list file
genbankread	Read data from GenBank file
genpeptread	Read data from GenPept file
geoseriesread	Read Gene Expression Omnibus (GEO) Series (GSE) format data
geosoftread	Read Gene Expression Omnibus (GEO) SOFT format data
getblast	Retrieve BLAST report from NCBI Web site
getembl	Retrieve sequence information from EMBL database
getgenbank	Retrieve sequence information from GenBank database
getgenpept	Retrieve sequence information from GenPept database
getgeodata	Retrieve Gene Expression Omnibus (GEO) format data
gethmmalignment	Retrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database
gethmmprof	Retrieve hidden Markov model (HMM) profile from PFAM database
gethmmtree	Retrieve phylogenetic tree data from PFAM database
getpdb	Retrieve protein structure data from Protein Data Bank (PDB) database
goannotread	Read annotations from Gene Ontology annotated file
gprread	Read microarray data from GenePix Results (GPR) file
ilmnbsread	Read gene expression data exported from Illumina BeadStudio software
imageneread	Read microarray data from ImaGene Results file
jcampread	Read JCAMP-DX-formatted files
multialignread	Read multiple sequence alignment file
multialignwrite	Write multiple alignment to file
mzcdfinfo	Return information about netCDF file containing mass spectrometry data
mzcdfread	Read mass spectrometry data from netCDF file
mzxmlinfo	Return information about mzXML file
mzxmlread	Read data from mzXML file
pdbread	Read data from Protein Data Bank (PDB) file
pdbwrite	Write to file using Protein Data Bank (PDB) format
pfamhmmread	Read data from PFAM HMM-formatted file
phytreeread	Read phylogenetic tree file
phytreewrite	Write phylogenetic tree object to Newick-formatted file
saminfo	Return information about Sequence Alignment/Map (SAM) file
samread	Read data from Sequence Alignment/Map (SAM) file
scfread	Read trace data from SCF file
sffinfo	Return information about SFF file
sffread	Read data from SFF file
sptread	Read data from SPOT file
tgspcinfo	Return information about SPC file
tgspcread	Read data from SPC file

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Data Visualization

cghfreqplot	Display frequency of DNA copy number alterations across multiple samples
clustergram	Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
featuresmap	Draw linear or circular map of features from GenBank structure
HeatMap	Display heat map of matrix data and create HeatMap object
maboxplot	Create box plot for microarray data
maimage	Spatial image for microarray data
mairplot	Create intensity versus ratio scatter plot of microarray data
maloglog	Create loglog plot of microarray data
mapcaplot	Create Principal Component Analysis (PCA) plot of microarray data
mavolcanoplot	Create significance versus gene expression ratio (fold change) scatter plot of microarray data
microplateplot	Display visualization of microtiter plate
molviewer	Display and manipulate 3-D molecule structure
msdotplot	Plot set of peak lists from LC/MS or GC/MS data set
msheatmap	Create pseudocolor image of set of mass spectra
msviewer	Explore mass spectrum or set of mass spectra
multialignviewer	Display and interactively adjust multiple sequence alignment
ntdensity	Plot density of nucleotides along sequence
pdbdistplot	Visualize intermolecular distances in Protein Data Bank (PDB) file
probesetplot	Plot Affymetrix probe set intensity values
proteinplot	Open Protein Plot window to investigate properties of amino acid sequence
proteinpropplot	Plot properties of amino acid sequence
ramachandran	Draw Ramachandran plot for Protein Data Bank (PDB) data
rnaplot	Draw secondary structure of RNA sequence
seqdotplot	Create dot plot of two sequences
seqtool	Open Sequence Tool window to interactively explore biological sequences
showalignment	Display color-coded sequence alignment
showhmmprof	Plot hidden Markov model (HMM) profile
traceplot	Draw nucleotide trace plots

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Trace Tools

scfread	Read trace data from SCF file
traceplot	Draw nucleotide trace plots

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Sequence Conversion

aa2int	Convert amino acid sequence from letter to integer representation
aa2nt	Convert amino acid sequence to nucleotide sequence
aminolookup	Find amino acid codes, integers, abbreviations, names, and codons
baselookup	Find nucleotide codes, integers, names, and complements
dna2rna	Convert DNA sequence to RNA sequence
int2aa	Convert amino acid sequence from integer to letter representation
int2nt	Convert nucleotide sequence from integer to letter representation
nt2aa	Convert nucleotide sequence to amino acid sequence
nt2int	Convert nucleotide sequence from letter to integer representation
rna2dna	Convert RNA sequence to DNA sequence
rnaconvert	Convert secondary structure of RNA sequence between bracket and matrix notations
seq2regexp	Convert sequence with ambiguous characters to regular expression
seqcomplement	Calculate complementary strand of nucleotide sequence
seqrcomplement	Calculate reverse complementary strand of nucleotide sequence
seqreverse	Calculate reverse strand of nucleotide sequence

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Sequence Utilities

aminolookup	Find amino acid codes, integers, abbreviations, names, and codons
baselookup	Find nucleotide codes, integers, names, and complements
blastlocal	Perform search on local BLAST database to create BLAST report
blastncbi	Create remote NCBI BLAST report request ID or link to NCBI BLAST report
cleave	Cleave amino acid sequence with enzyme
cleavelookup	Find cleavage rule for enzyme or compound
featuresparse	Parse features from GenBank, GenPept, or EMBL data
geneticcode	Return nucleotide codon to amino acid mapping for genetic code
joinseq	Join two sequences to produce shortest supersequence
oligoprop	Calculate sequence properties of DNA oligonucleotide
palindromes	Find palindromes in sequence
pdbdistplot	Visualize intermolecular distances in Protein Data Bank (PDB) file
proteinplot	Open Protein Plot window to investigate properties of amino acid sequence
proteinpropplot	Plot properties of amino acid sequence
ramachandran	Draw Ramachandran plot for Protein Data Bank (PDB) data
randseq	Generate random sequence from finite alphabet
rebasecuts	Find restriction enzymes that cut nucleotide sequence
restrict	Split nucleotide sequence at restriction site
revgeneticcode	Return reverse mapping (amino acid to nucleotide codon) for genetic code
rnafold	Predict minimum free-energy secondary structure of RNA sequence
seqconsensus	Calculate consensus sequence
seqdisp	Format long sequence output for easy viewing
seqinsertgaps	Insert gaps into nucleotide or amino acid sequence
seqlogo	Display sequence logo for nucleotide or amino acid sequences
seqmatch	Find matches for every string in library
seqprofile	Calculate sequence profile from set of multiply aligned sequences
seqshoworfs	Display open reading frames in sequence

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Sequence Statistics

aacount	Count amino acids in sequence
aminolookup	Find amino acid codes, integers, abbreviations, names, and codons
basecount	Count nucleotides in sequence
baselookup	Find nucleotide codes, integers, names, and complements
codonbias	Calculate codon frequency for each amino acid coded for in nucleotide sequence
codoncount	Count codons in nucleotide sequence
cpgisland	Locate CpG islands in DNA sequence
dimercount	Count dimers in nucleotide sequence
isoelectric	Estimate isoelectric point for amino acid sequence
molweight	Calculate molecular weight of amino acid sequence
nmercount	Count n-mers in nucleotide or amino acid sequence
ntdensity	Plot density of nucleotides along sequence
seqshowwords	Graphically display words in sequence
seqwordcount	Count number of occurrences of word in sequence

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Sequence Visualization

featuresmap	Draw linear or circular map of features from GenBank structure
multialignviewer	Display and interactively adjust multiple sequence alignment
rnaplot	Draw secondary structure of RNA sequence
seqdotplot	Create dot plot of two sequences
seqtool	Open Sequence Tool window to interactively explore biological sequences
showalignment	Display color-coded sequence alignment

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Pairwise Sequence Alignment

fastaread	Read data from FASTA file
localalign	Return local optimal and suboptimal alignments between two sequences
multialignviewer	Display and interactively adjust multiple sequence alignment
nwalign	Globally align two sequences using Needleman-Wunsch algorithm
seqdotplot	Create dot plot of two sequences
showalignment	Display color-coded sequence alignment
swalign	Locally align two sequences using Smith-Waterman algorithm

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Multiple Sequence Alignment

fastaread	Read data from FASTA file
multialign	Align multiple sequences using progressive method
multialignread	Read multiple sequence alignment file
multialignviewer	Display and interactively adjust multiple sequence alignment
multialignwrite	Write multiple alignment to file
profalign	Align two profiles using Needleman-Wunsch global alignment
seqpdist	Calculate pairwise distance between sequences
showalignment	Display color-coded sequence alignment

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Scoring Matrices

blosum	Return BLOSUM scoring matrix
dayhoff	Return Dayhoff scoring matrix
gonnet	Return Gonnet scoring matrix
nuc44	Return NUC44 scoring matrix for nucleotide sequences
pam	Return Point Accepted Mutation (PAM) scoring matrix

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Phylogenetic Tree Tools

dnds	Estimate synonymous and nonsynonymous substitution rates
dndsml	Estimate synonymous and nonsynonymous substitution rates using maximum likelihood method
gethmmtree	Retrieve phylogenetic tree data from PFAM database
phytreeread	Read phylogenetic tree file
phytreetool	View, edit, and explore phylogenetic tree data
phytreewrite	Write phylogenetic tree object to Newick-formatted file
seqinsertgaps	Insert gaps into nucleotide or amino acid sequence
seqlinkage	Construct phylogenetic tree from pairwise distances
seqneighjoin	Neighbor-joining method for phylogenetic tree reconstruction
seqpdist	Calculate pairwise distance between sequences

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Phylogenetic Tree Methods

Following are methods to use with a phytree object.

cluster (phytree)	Validate clusters in phylogenetic tree
get (phytree)	Retrieve information about phylogenetic tree object
getbyname (phytree)	Branches and leaves from phytree object
getcanonical (phytree)	Calculate canonical form of phylogenetic tree
getmatrix (phytree)	Convert phytree object into relationship matrix
getnewickstr (phytree)	Create Newick-formatted string
pdist (phytree)	Calculate pairwise patristic distances in phytree object
plot (phytree)	Draw phylogenetic tree
prune (phytree)	Remove branch nodes from phylogenetic tree
reorder (phytree)	Reorder leaves of phylogenetic tree
reroot (phytree)	Change root of phylogenetic tree
select (phytree)	Select tree branches and leaves in phytree object
subtree (phytree)	Extract phylogenetic subtree
view (phytree)	View phylogenetic tree
weights (phytree)	Calculate weights for phylogenetic tree

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Graph Theory

graphallshortestpaths	Find all shortest paths in graph
graphconncomp	Find strongly or weakly connected components in graph
graphisdag	Test for cycles in directed graph
graphisomorphism	Find isomorphism between two graphs
graphisspantree	Determine if tree is spanning tree
graphmaxflow	Calculate maximum flow in directed graph
graphminspantree	Find minimal spanning tree in graph
graphpred2path	Convert predecessor indices to paths
graphshortestpath	Solve shortest path problem in graph
graphtopoorder	Perform topological sort of directed acyclic graph
graphtraverse	Traverse graph by following adjacent nodes

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Graph Visualization Methods

Following are methods to use with a biograph object.

allshortestpaths (biograph)	Find all shortest paths in biograph object
conncomp (biograph)	Find strongly or weakly connected components in biograph object
dolayout (biograph)	Calculate node positions and edge trajectories
get (biograph)	Retrieve information about biograph object
getancestors (biograph)	Find ancestors in biograph object
getdescendants (biograph)	Find descendants in biograph object
getedgesbynodeid (biograph)	Get handles to edges in biograph object
getmatrix (biograph)	Get connection matrix from biograph object
getnodesbyid (biograph)	Get handles to nodes
getrelatives (biograph)	Find relatives in biograph object
isdag (biograph)	Test for cycles in biograph object
isomorphism (biograph)	Find isomorphism between two biograph objects
isspantree (biograph)	Determine if tree created from biograph object is spanning tree
maxflow (biograph)	Calculate maximum flow in biograph object
minspantree (biograph)	Find minimal spanning tree in biograph object
set (biograph)	Set property of biograph object
shortestpath (biograph)	Solve shortest path problem in biograph object
topoorder (biograph)	Perform topological sort of directed acyclic graph extracted from biograph object
traverse (biograph)	Traverse biograph object by following adjacent nodes
view (biograph)	Draw figure from biograph object

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Gene Ontology

goannotread	Read annotations from Gene Ontology annotated file
num2goid	Convert numbers to Gene Ontology IDs

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Gene Ontology Methods

Following are methods to use with a geneont object.

getancestors (geneont)	Find terms that are ancestors of specified Gene Ontology (GO) term
getdescendants (geneont)	Find terms that are descendants of specified Gene Ontology (GO) term
getmatrix (geneont)	Convert geneont object into relationship matrix
getrelatives (geneont)	Find terms that are relatives of specified Gene Ontology (GO) term

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Protein Analysis

aacount	Count amino acids in sequence
aminolookup	Find amino acid codes, integers, abbreviations, names, and codons
atomiccomp	Calculate atomic composition of protein
cleave	Cleave amino acid sequence with enzyme
cleavelookup	Find cleavage rule for enzyme or compound
evalrasmolscript	Send RasMol script commands to Molecule Viewer window
isoelectric	Estimate isoelectric point for amino acid sequence
isotopicdist	Calculate high-resolution isotope mass distribution and density function
molviewer	Display and manipulate 3-D molecule structure
molweight	Calculate molecular weight of amino acid sequence
pdbdistplot	Visualize intermolecular distances in Protein Data Bank (PDB) file
pdbsuperpose	Superpose 3-D structures of two proteins
pdbtransform	Apply linear transformation to 3-D structure of molecule
proteinplot	Open Protein Plot window to investigate properties of amino acid sequence
proteinpropplot	Plot properties of amino acid sequence
ramachandran	Draw Ramachandran plot for Protein Data Bank (PDB) data

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Profile Hidden Markov Models

gethmmalignment	Retrieve multiple sequence alignment associated with hidden Markov model (HMM) profile from PFAM database
gethmmprof	Retrieve hidden Markov model (HMM) profile from PFAM database
gethmmtree	Retrieve phylogenetic tree data from PFAM database
hmmprofalign	Align query sequence to profile using hidden Markov model alignment
hmmprofestimate	Estimate profile hidden Markov model (HMM) parameters using pseudocounts
hmmprofgenerate	Generate random sequence drawn from profile hidden Markov model (HMM)
hmmprofmerge	Concatenate prealigned strings of several sequences to profile hidden Markov model (HMM)
hmmprofstruct	Create or edit hidden Markov model (HMM) profile structure
pfamhmmread	Read data from PFAM HMM-formatted file
showhmmprof	Plot hidden Markov model (HMM) profile

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Microarray File Formats

affyprobeseqread	Read data file containing probe sequence information for Affymetrix GeneChip array
affyread	Read microarray data from Affymetrix GeneChip file
affysnpannotread	Read Affymetrix Mapping DNA array data from CSV-format annotation file
agferead	Read Agilent Feature Extraction Software file
celintensityread	Read probe intensities from Affymetrix CEL files
galread	Read microarray data from GenePix array list file
geoseriesread	Read Gene Expression Omnibus (GEO) Series (GSE) format data
geosoftread	Read Gene Expression Omnibus (GEO) SOFT format data
getgeodata	Retrieve Gene Expression Omnibus (GEO) format data
gprread	Read microarray data from GenePix Results (GPR) file
ilmnbsread	Read gene expression data exported from Illumina BeadStudio software
imageneread	Read microarray data from ImaGene Results file
sptread	Read data from SPOT file

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Microarray Utilities

affysnpintensitysplit	Split Affymetrix SNP probe intensity information for alleles A and B
affysnpquartets	Create table of SNP probe quartet results for Affymetrix probe set
ilmnbslookup	Look up Illumina BeadStudio target (probe) sequence and annotation information
magetfield	Extract data from microarray structure
probelibraryinfo	Create table of probe set library information
probesetlink	Display probe set information on NetAffx Web site
probesetlookup	Look up information for Affymetrix probe set
probesetplot	Plot Affymetrix probe set intensity values
probesetvalues	Create table of Affymetrix probe set intensity values

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Microarray Data Analysis and Visualization

cghcbs	Perform circular binary segmentation (CBS) on array-based comparative genomic hybridization (aCGH) data
cghfreqplot	Display frequency of DNA copy number alterations across multiple samples
chromosomeplot	Plot chromosome ideogram with G-banding pattern
clustergram	Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
HeatMap	Display heat map of matrix data and create HeatMap object
maboxplot	Create box plot for microarray data
mafdr	Estimate false discovery rate (FDR) of differentially expressed genes from two experimental conditions or phenotypes
maimage	Spatial image for microarray data
mairplot	Create intensity versus ratio scatter plot of microarray data
maloglog	Create loglog plot of microarray data
mapcaplot	Create Principal Component Analysis (PCA) plot of microarray data
mattest	Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mavolcanoplot	Create significance versus gene expression ratio (fold change) scatter plot of microarray data
microplateplot	Display visualization of microtiter plate
probesetplot	Plot Affymetrix probe set intensity values
redbluecmap	Create red and blue colormap
redgreencmap	Create red and green colormap

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Microarray Normalization and Filtering

affygcrma	Perform GC Robust Multi-array Average (GCRMA) procedure on Affymetrix microarray probe-level data
affyinvarsetnorm	Perform rank invariant set normalization on probe intensities from multiple Affymetrix CEL or DAT files
affyprobeaffinities	Compute Affymetrix probe affinities from their sequences and MM probe intensities
affyrma	Perform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data
exprprofrange	Calculate range of gene expression profiles
exprprofvar	Calculate variance of gene expression profiles
gcrma	Perform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data
gcrmabackadj	Perform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information
geneentropyfilter	Remove genes with low entropy expression values
genelowvalfilter	Remove gene profiles with low absolute values
generangefilter	Remove gene profiles with small profile ranges
genevarfilter	Filter genes with small profile variance
mainvarsetnorm	Perform rank invariant set normalization on gene expression values from two experimental conditions or phenotypes
malowess	Smooth microarray data using Lowess method
manorm	Normalize microarray data
quantilenorm	Quantile normalization over multiple arrays
rmabackadj	Perform background adjustment on Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
rmasummary	Calculate gene expression values from Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure
zonebackadj	Perform background adjustment on Affymetrix microarray probe-level data using zone-based method

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BioIndexedFile Methods

Following are methods to use with a BioIndexedFile object.

getEntryByIndex (BioIndexedFile)	Retrieve entries from source file associated with BioIndexedFile object using numeric index
getEntryByKey (BioIndexedFile)	Retrieve entries from source file associated with BioIndexedFile object using alphanumeric key
getIndexByKey (BioIndexedFile)	Retrieve indices from source file associated with BioIndexedFile object using alphanumeric key
getKeys (BioIndexedFile)	Retrieve alphanumeric keys from source file associated with BioIndexedFile object
read (BioIndexedFile)	Read one or more entries from source file associated with BioIndexedFile object

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BioRead Methods

Following are methods to use with a BioRead object.

combine (BioRead)	Combine two objects
get (BioRead)	Retrieve property of object
getHeader (BioRead)	Retrieve sequence headers from object
getName (BioRead)	Retrieve name of object
getNSeqs (BioRead)	Retrieve number of sequences in object
getQuality (BioRead)	Retrieve sequence quality scores from object
getSequence (BioRead)	Retrieve sequences from object
getSubsequence (BioRead)	Retrieve partial sequences from object
getSubset (BioRead)	Retrieve elements from object
set (BioRead)	Set property of object
setHeader (BioRead)	Set sequence headers for object
setName (BioRead)	Set name of object
setQuality (BioRead)	Set sequence quality scores for object
setSequence (BioRead)	Set sequences for object
setSubsequence (BioRead)	Set partial sequences for object
setSubset (BioRead)	Set elements for object

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BioMap Methods

Following are methods to use with a BioMap object.

filterByFlag (BioMap)	Filter sequence reads by SAM flag
getAlignment (BioMap)	Construct alignment represented in BioMap object
getCoverage (BioMap)	Compute read coverage in BioMap object
getFlag (BioMap)	Retrieve read sequence flags from BioMap object
getInfo (BioMap)	Retrieve information for single element of BioMap object
getMappingQuality (BioMap)	Retrieve sequence mapping quality scores from BioMap object
getReference (BioMap)	Retrieve reference sequence from BioMap object
getSignature (BioMap)	Retrieve signature (alignment information) from BioMap object
getStart (BioMap)	Retrieve start positions of aligned read sequences from BioMap object
getStop (BioMap)	Compute stop positions of aligned read sequences from BioMap object
setFlag (BioMap)	Set read sequence flags for BioMap object
setMappingQuality (BioMap)	Set sequence mapping quality scores for BioMap object
setReference (BioMap)	Set name of reference sequence for BioMap object
setSignature (BioMap)	Set signature (alignment information) for BioMap object
setStart (BioMap)	Set start positions of aligned read sequences in BioMap object

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HeatMap Methods

Following are methods to use with a HeatMap object.

addTitle (HeatMap)	Add title to heat map
addXLabel (HeatMap)	Label x-axis of heat map
addYLabel (HeatMap)	Label y-axis of heat map
plot (HeatMap)	Render heat map for HeatMap object
view (HeatMap)	View heat map of HeatMap object

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Clustergram Methods

Following are methods to use with a clustergram object.

addTitle (clustergram)	Add title to clustergram
addXLabel (clustergram)	Label x-axis of clustergram
addYLabel (clustergram)	Label y-axis of clustergram
clusterGroup (clustergram)	Select cluster group
get (clustergram)	Retrieve information about clustergram object
plot (clustergram)	Render clustergram and dendrograms for clustergram object
set (clustergram)	Set property of clustergram object
view (clustergram)	View clustergram and dendrograms of clustergram object

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ExpressionSet Methods

Following are methods to use with an ExpressionSet object.

abstract (bioma.ExpressionSet)	Retrieve or set abstract describing experiment in ExpressionSet object
elementData (bioma.ExpressionSet)	Retrieve or set data element (DataMatrix object) in ExpressionSet object
elementNames (bioma.ExpressionSet)	Retrieve or set element names of DataMatrix objects in ExpressionSet object
expressions (bioma.ExpressionSet)	Retrieve or set Expressions DataMatrix object from ExpressionSet object
exprWrite (bioma.ExpressionSet)	Write expression values in ExpressionSet object to text file
exptData (bioma.ExpressionSet)	Retrieve or set experiment data in ExpressionSet object
exptInfo (bioma.ExpressionSet)	Retrieve or set experiment information in ExpressionSet object
featureData (bioma.ExpressionSet)	Retrieve or set feature metadata in ExpressionSet object
featureNames (bioma.ExpressionSet)	Retrieve or set feature names in ExpressionSet object
featureVarDesc (bioma.ExpressionSet)	Retrieve or set feature variable descriptions in ExpressionSet object
featureVarNames (bioma.ExpressionSet)	Retrieve or set feature variable names in ExpressionSet object
featureVarValues (bioma.ExpressionSet)	Retrieve or set feature variable data values in ExpressionSet object
pubMedID (bioma.ExpressionSet)	Retrieve or set PubMed IDs in ExpressionSet object
sampleData (bioma.ExpressionSet)	Retrieve or set sample metadata in ExpressionSet object
sampleNames (bioma.ExpressionSet)	Retrieve or set sample names in ExpressionSet object
sampleVarDesc (bioma.ExpressionSet)	Retrieve or set sample variable descriptions in ExpressionSet object
sampleVarNames (bioma.ExpressionSet)	Retrieve or set sample variable names in ExpressionSet object
sampleVarValues (bioma.ExpressionSet)	Retrieve or set sample variable values in ExpressionSet object
size (bioma.ExpressionSet)	Return size of ExpressionSet object

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ExptData Methods

Following are methods to use with an ExptData object.

combine (bioma.data.ExptData)	Combine two ExptData objects
dmNames (bioma.data.ExptData)	Retrieve or set Name properties of DataMatrix objects in ExptData object
elementData (bioma.data.ExptData)	Retrieve or set data element (DataMatrix object) in ExptData object
elementNames (bioma.data.ExptData)	Retrieve or set element names of DataMatrix objects in ExptData object
featureNames (bioma.data.ExptData)	Retrieve or set feature names in ExptData object
isempty (bioma.data.ExptData)	Determine whether ExptData object is empty
sampleNames (bioma.data.ExptData)	Retrieve or set sample names in ExptData object
size (bioma.data.ExptData)	Return size of ExptData object

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DataMatrix Methods

Following are methods to use with a DataMatrix object.

colnames (DataMatrix)	Retrieve or set column names of DataMatrix object
disp (DataMatrix)	Display DataMatrix object
dmarrayfun (DataMatrix)	Apply function to each element in DataMatrix object
dmbsxfun (DataMatrix)	Apply element-by-element binary operation to two DataMatrix objects with singleton expansion enabled
dmwrite (DataMatrix)	Write DataMatrix object to text file
double (DataMatrix)	Convert DataMatrix object to double-precision array
eq (DataMatrix)	Test DataMatrix objects for equality
ge (DataMatrix)	Test DataMatrix objects for greater than or equal to
get (DataMatrix)	Retrieve information about DataMatrix object
gt (DataMatrix)	Test DataMatrix objects for greater than
horzcat (DataMatrix)	Concatenate DataMatrix objects horizontally
isequal (DataMatrix)	Test DataMatrix objects for equality
isequalwithequalnans (DataMatrix)	Test DataMatrix objects for equality, treating NaNs as equal
ldivide (DataMatrix)	Left array divide DataMatrix objects
le (DataMatrix)	Test DataMatrix objects for less than or equal to
lt (DataMatrix)	Test DataMatrix objects for less than
max (DataMatrix)	Return maximum values in DataMatrix object
mean (DataMatrix)	Return average or mean values in DataMatrix object
median (DataMatrix)	Return median values in DataMatrix object
min (DataMatrix)	Return minimum values in DataMatrix object
minus (DataMatrix)	Subtract DataMatrix objects
ndims (DataMatrix)	Return number of dimensions in DataMatrix object
ne (DataMatrix)	Test DataMatrix objects for inequality
numel (DataMatrix)	Return number of elements in DataMatrix object
plot (DataMatrix)	Draw 2-D line plot of DataMatrix object
plus (DataMatrix)	Add DataMatrix objects
power (DataMatrix)	Array power DataMatrix objects
rdivide (DataMatrix)	Right array divide DataMatrix objects
rownames (DataMatrix)	Retrieve or set row names of DataMatrix object
set (DataMatrix)	Set property of DataMatrix object
single (DataMatrix)	Convert DataMatrix object to single-precision array
sortcols (DataMatrix)	Sort columns of DataMatrix object in ascending or descending order
sortrows (DataMatrix)	Sort rows of DataMatrix object in ascending or descending order
std (DataMatrix)	Return standard deviation values in DataMatrix object
sum (DataMatrix)	Return sum of elements in DataMatrix object
times (DataMatrix)	Multiply DataMatrix objects
var (DataMatrix)	Return variance values in DataMatrix object
vertcat (DataMatrix)	Concatenate DataMatrix objects vertically

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MetaData Methods

Following are methods to use with a MetaData object.

combine (bioma.data.MetaData)	Combine two MetaData objects
isempty (bioma.data.MetaData)	Determine whether MetaData object is empty
sampleNames (bioma.data.MetaData)	Retrieve or set sample names in MetaData object
size (bioma.data.MetaData)	Return size of MetaData object
variableDesc (bioma.data.MetaData)	Retrieve or set variable descriptions for samples in MetaData object
variableNames (bioma.data.MetaData)	Retrieve or set variable names for samples in MetaData object
variableValues (bioma.data.MetaData)	Retrieve or set variable values for samples in MetaData object
varValuesTable (bioma.data.MetaData)	Create 2-D graphic table GUI of variable values in MetaData object

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MIAME Methods

Following are methods to use with a MIAME object.

combine (bioma.data.MIAME)	Combine two MIAME objects
isempty (bioma.data.MIAME)	Determine whether MIAME object is empty

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Statistical Learning

classperf	Evaluate performance of classifier
crossvalind	Generate cross-validation indices
knnclassify	Classify data using nearest neighbor method
knnimpute	Impute missing data using nearest-neighbor method
optimalleaforder	Determine optimal leaf ordering for hierarchical binary cluster tree
randfeatures	Generate randomized subset of features
rankfeatures	Rank key features by class separability criteria
svmclassify	Classify data using support vector machine
svmsmoset	Create or edit Sequential Minimal Optimization (SMO) options structure
svmtrain	Train support vector machine classifier

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Mass Spectrometry

isotopicdist	Calculate high-resolution isotope mass distribution and density function
jcampread	Read JCAMP-DX-formatted files
msalign	Align peaks in signal to reference peaks
msbackadj	Correct baseline of signal with peaks
msdotplot	Plot set of peak lists from LC/MS or GC/MS data set
msheatmap	Create pseudocolor image of set of mass spectra
mslowess	Smooth signal with peaks using nonparametric method
msnorm	Normalize set of signals with peaks
mspalign	Align mass spectra from multiple peak lists from LC/MS or GC/MS data set
mspeaks	Convert raw peak data to peak list (centroided data)
msppresample	Resample signal with peaks while preserving peaks
msresample	Resample signal with peaks
mssgolay	Smooth signal with peaks using least-squares polynomial
msviewer	Explore mass spectrum or set of mass spectra
mzcdf2peaks	Convert mzCDF structure to peak list
mzcdfinfo	Return information about netCDF file containing mass spectrometry data
mzcdfread	Read mass spectrometry data from netCDF file
mzxml2peaks	Convert mzXML structure to peak list
mzxmlinfo	Return information about mzXML file
mzxmlread	Read data from mzXML file
samplealign	Align two data sets containing sequential observations by introducing gaps
tgspcinfo	Return information about SPC file
tgspcread	Read data from SPC file

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Bioanalytics

jcampread	Read JCAMP-DX-formatted files
msalign	Align peaks in signal to reference peaks
msbackadj	Correct baseline of signal with peaks
mslowess	Smooth signal with peaks using nonparametric method
msnorm	Normalize set of signals with peaks
mspeaks	Convert raw peak data to peak list (centroided data)
msppresample	Resample signal with peaks while preserving peaks
msresample	Resample signal with peaks
mssgolay	Smooth signal with peaks using least-squares polynomial
tgspcinfo	Return information about SPC file
tgspcread	Read data from SPC file

Class Reference

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