Tool to fit Probe Level Models.
Accessors for physical array coordinates.
Methods for class CopyNumberSet.
RMA - Robust Multichip Average algorithm
Methods for class AssayData in the oligoClasses package
Get the connection to the SQLite Database
Summarization of SNP data
Virtual Class for Lists of eSets
Methods for Log-Ratio plotting
Defunct Functions in Package 'oligo'
Retrieve Platform Design object
Accessor for chromosome information
Access the allele information for PM probes.
Gets a bar of a given length.
DEPRECATED FUNCTIONS.
Cluster and large dataset management utilities.
Cluster and large dataset management utilities.
Simplified interface to PLM.
Platform Information
SnpCnvQSet Example
Available Affymetrix platforms for SNP arrays
Simplified interface to RMA.
Sample names for FeatureSet-like objects
lapply-like function that parallelizes code when possible.
Container for objects with genomic annotation on SNPs
Set/check large dataset options.
Genome Build Information
oligoClasses Deprecated
Manufacturer ID for FeatureSet-like objects.
Checks whether a eSet-derived class is ordered by chromosome and
physical position
Tools to distribute objects across nodes or by length.
Accessor for the 'exprs' slot
Batch-level summary of SNP flags.
Methods for Function isSnp in package oligoClasses~~
MA plots
Accessors and replacement methods for the intensity/PM/MM/BG matrices.
Initialize big matrices/vectors.
Class "ff_matrix"
Boxplot
Display a pseudo-image of a microarray chip
Create ff objects.
Load chromosome sequence lengths for UCSC genome build hg18 or hg19
Tools for microarray preprocessing.
Accessor to feature names
Date of scan
Function to get CRLMM summaries saved to disk
GenomeAnnotatedDataFrameFrom-methods
Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses
Preprocessing SNP Arrays
NetAffx Biological Annotations
Accessor for slot assayDataList in Package oligoClasses Access the fragment length for PM probes.
Methods for GRanges objects
Checks to see whether an object exists and, if not, executes the appropriate function.
SummarizedExperiment-methods
Methods for RangedSummarizedExperiment objects
Create a list of assay data elements
Create design matrix for sequences
Class "SnpSuperSet"
Checks if oligo/crlmm can use parallel resources.
Miscellaneous generics. Methods defined in packages that depend
on oligoClasses
Basic data elements required for the HMM
Check if object is an ff-matrix object.
The batch variable for the samples.
Create set of colors, interpolating through a set of preferred colors.
Accessor to the strand information
Accessors and methods for SnpSet objects
Helper function to load packages.
Parser to XYS files
getAffinitySplineCoefficients
Estimate affinity coefficients.
Probe information selector.
Class "DBPDInfo"
Extracts complete cel file name from a CNSet object
Open and close methods for matrices and numeric vectors
Get packages from BioConductor.
Class "ffdf"
An example instance of oligoSnpSet class
Annotation Packages
Converts chromosome to integer
GenomeAnnotatedDataFrame-class
Class "GenomeAnnotatedDataFrame"
Class "BeadStudioSet"
Supress package startup messages when loading a library
Array type
SnpQSet Example
Helper function to extract color information for filenames on
NimbleGen arrays.
Class "oligoPLM"
Get container information for NimbleGen Tiling Arrays.
List classes with assay data listed by chromosome
"FeatureSet" and "FeatureSet" Extensions
Methods for function chromosome in package oligoClasses
SnpFeatureSet Example
Sequence Base Contents
Compute average log-intensities / log-ratios
Information on Fragment Length
DEPRECATED FUNCTIONS.
Package loaders for clusters.
Class "CNSet"
Methods for function position in Package oligoClasses
Cel file dates
Accessor for batch statistics uses for copy number estimation
and storage of model parameters
Accessor for slot featureDataList in Package oligoClasses ~~ Check if package is loaded.
Number of samples for FeatureSet-like objects.
Coerce numeric matrix (or array) to a matrix (array) of integers, retaining dimnames.
Class "AlleleSet"
Construct a GRanges object from several possible feature-level classes
Density estimate
Probe Sequeces
Genotype Calls
Compute and plot nucleotide profile.
The oligo package: a tool for low-level analysis of oligonucleotide arrays
Methods for P/A Calls
List XYS files
Parser to CEL files
Read summaries generated by crlmm
Accessor to position information
Class "CopyNumberSet"
eSetList class
ExpressionFeatureSet Object
Class "SnpSet2"
Functions to convert probabilities to integers, or integers to probabilities.
Class "ff_or_matrix"
Array Geometry Information
Accessors for PM, MM or background probes indices.
Methods for oligoSnpSet class
List CEL files.