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oligo (version 1.36.1)

Preprocessing tools for oligonucleotide arrays

Description

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

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Version

Version

1.36.1

License

LGPL (>= 2)

Maintainer

Benilton Carvalho

Last Published

February 15th, 2017

Functions in oligo (1.36.1)

fitProbeLevelModel

Tool to fit Probe Level Models.

Accessors for physical array coordinates.

CopyNumberSet-methods

Methods for class CopyNumberSet.

RMA - Robust Multichip Average algorithm

AssayData-methods

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'

getPlatformDesign

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-methods

Platform Information

SnpCnvQSet Example

Available Affymetrix platforms for SNP arrays

Simplified interface to RMA.

sampleNames-methods

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-methods

Manufacturer ID for FeatureSet-like objects.

Checks whether a eSet-derived class is ordered by chromosome and physical position

splitIndicesByLength

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~~

Accessors and replacement methods for the intensity/PM/MM/BG matrices.

initializeBigMatrix

Initialize big matrices/vectors.

ff_matrix-class

Class "ff_matrix"

Display a pseudo-image of a microarray chip

Create ff objects.

getSequenceLengths

Load chromosome sequence lengths for UCSC genome build hg18 or hg19

Tools for microarray preprocessing.

Accessor to feature names

getCrlmmSummaries

Function to get CRLMM summaries saved to disk

GenomeAnnotatedDataFrameFrom-methods

Methods for Function GenomeAnnotatedDataFrameFrom in Package oligoClasses

Preprocessing SNP Arrays

NetAffx Biological Annotations

assayDataList-methods

Accessor for slot assayDataList in Package oligoClasses

pmFragmentLength

Access the fragment length for PM probes.

GRanges-methods

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

sequenceDesignMatrix

Create design matrix for sequences

SnpSuperSet-class

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

requireAnnotation

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

fileConnections

Open and close methods for matrices and numeric vectors

Get packages from BioConductor.

An example instance of oligoSnpSet class

annotationPackages

Annotation Packages

chromosome2integer

Converts chromosome to integer

GenomeAnnotatedDataFrame-class

Class "GenomeAnnotatedDataFrame"

BeadStudioSet-class

Class "BeadStudioSet"

Supress package startup messages when loading a library

SnpQSet Example

getNgsColorsInfo

Helper function to extract color information for filenames on NimbleGen arrays.

Class "oligoPLM"

Get container information for NimbleGen Tiling Arrays.

BeadStudioSetList-class

List classes with assay data listed by chromosome

FeatureSet-class

"FeatureSet" and "FeatureSet" Extensions

chromosome-methods

Methods for function chromosome in package oligoClasses

SnpFeatureSet Example

Sequence Base Contents

Compute average log-intensities / log-ratios

pmFragmentLength-methods

Information on Fragment Length

requireClusterPkgSet

DEPRECATED FUNCTIONS. Package loaders for clusters.

position-methods

Methods for function position in Package oligoClasses

batchStatistics

Accessor for batch statistics uses for copy number estimation and storage of model parameters

featureDataList-methods

Accessor for slot featureDataList in Package oligoClasses ~~

isPackageLoaded

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.

AlleleSet-class

Class "AlleleSet"

makeFeatureGRanges

Construct a GRanges object from several possible feature-level classes

Density estimate

Compute and plot nucleotide profile.

The oligo package: a tool for low-level analysis of oligonucleotide arrays

Methods for P/A Calls

Parser to CEL files

Read summaries generated by crlmm

Accessor to position information

CopyNumberSet-class

Class "CopyNumberSet"

ExpressionFeatureSet Object

Class "SnpSet2"

Functions to convert probabilities to integers, or integers to probabilities.

ff_or_matrix-class

Class "ff_or_matrix"

Array Geometry Information

Accessors for PM, MM or background probes indices.

oligoSnpSet-methods

Methods for oligoSnpSet class

List CEL files.