Preprocessing tools for oligonucleotide arrays.

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Documentation for package ‘oligo’ version 1.14.0

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B C D G H I J L M N P R S

-- --

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

-- B --

backgroundCorrect Tools for microarray preprocessing
backgroundCorrect-method Tools for microarray preprocessing
backgroundCorrect-methods Tools for microarray preprocessing
basecontent Sequence Base Contents
basicRMA Simplified Interface to RMA
bg Accessors and replacement methods for the PM/MM/BG matrices.
bg-method Accessors and replacement methods for the PM/MM/BG matrices.
bg<- Accessors and replacement methods for the PM/MM/BG matrices.
bg<--method Accessors and replacement methods for the PM/MM/BG matrices.
bgindex Accessors for PM, MM or background probes indices.
bgindex-method Accessors for PM, MM or background probes indices.
bgSequence Probe Sequeces
bgSequence-method Probe Sequeces
boxplot-method Boxplot
boxplot-methods Boxplot

-- C --

chromosome Accessor for chromosome information
chromosome<- Accessor for chromosome information
chromosome<--method Accessor for chromosome information
cleanPlatformName Parser to CEL files
crlmm Genotype Calls

-- D --

darkColors Create set of colors, interpolating through a set of preferred colors.

-- G --

getAffinitySplineCoefficients Estimate affinity coefficients.
getBaseProfile Compute and plot nucleotide profile.
getContainer Get container information for NimbleGen Tiling Arrays.
getContainer-method Get container information for NimbleGen Tiling Arrays.
getContainer-methods Get container information for NimbleGen Tiling Arrays.
getCrlmmSummaries Function to get CRLMM summaries saved to disk
getNetAffx NetAffx Biological Annotations
getNetAffx-method NetAffx Biological Annotations
getNetAffx-methods NetAffx Biological Annotations
getNgsColorsInfo Helper function to extract color information for filenames on NimbleGen
getPD Retrieve Platform Design object
getPlatformDesign Retrieve Platform Design object
getPlatformDesign-method Retrieve Platform Design object
getX Accessors for physical array coordinates.
getX-method Accessors for physical array coordinates.
getX-methods Accessors for physical array coordinates.
getY Accessors for physical array coordinates.
getY-method Accessors for physical array coordinates.
getY-methods Accessors for physical array coordinates.

-- H --

hist-method Density estimate
hist-methods Density estimate

-- I --

image-method Display a pseudo-image of a microarray chip
image-methods Display a pseudo-image of a microarray chip

-- J --

justCRLMM Genotype Calls
justSNPRMA Summarization of SNP data

-- L --

list.xysfiles List XYS files

-- M --

MAplot MA plots
MAplot-method MA plots
MAplot-methods MA plots
mm Accessors and replacement methods for the PM/MM/BG matrices.
mm-method Accessors and replacement methods for the PM/MM/BG matrices.
mm<- Accessors and replacement methods for the PM/MM/BG matrices.
mm<--method Accessors and replacement methods for the PM/MM/BG matrices.
mmindex Accessors for PM, MM or background probes indices.
mmindex-method Accessors for PM, MM or background probes indices.
mmSequence Probe Sequeces
mmSequence-method Probe Sequeces

-- N --

normalize Tools for microarray preprocessing
normalize-method Tools for microarray preprocessing
normalize-methods Tools for microarray preprocessing
normalizeToTarget Tools for microarray preprocessing
normalizeToTarget-method Tools for microarray preprocessing
normalizeToTarget-methods Tools for microarray preprocessing

-- P --

plotM Methods for Log-Ratio plotting
plotM-method Methods for Log-Ratio plotting
plotM-methods Methods for Log-Ratio plotting
pm Accessors and replacement methods for the PM/MM/BG matrices.
pm-method Accessors and replacement methods for the PM/MM/BG matrices.
pm<- Accessors and replacement methods for the PM/MM/BG matrices.
pm<--method Accessors and replacement methods for the PM/MM/BG matrices.
pmAllele Access the allele information for PM probes.
pmAllele-method Access the allele information for PM probes.
pmChr Accessor for chromosome information
pmChr-method Accessor for chromosome information
pmFragmentLength Access the fragment length for PM probes.
pmFragmentLength-method Access the fragment length for PM probes.
pmindex Accessors for PM, MM or background probes indices.
pmindex-method Accessors for PM, MM or background probes indices.
pmOffset Accessor to position information
pmOffset-method Accessor to position information
pmPosition Accessor to position information
pmPosition-method Accessor to position information
pmSequence Probe Sequeces
pmSequence-method Probe Sequeces
pmStrand Accessor to the strand information
pmStrand-method Accessor to the strand information
probeNames Accessor to feature names
probeNames-method Accessor to feature names

-- R --

read.celfiles Parser to CEL files
read.celfiles2 Parser to CEL files
read.xysfiles Parser to XYS files
read.xysfiles2 Parser to XYS files
readSummaries Read summaries generated by crlmm
rma RMA - Robust Multichip Average algorithm
rma-method RMA - Robust Multichip Average algorithm
rma-methods RMA - Robust Multichip Average algorithm
runDate Date of scan
runDate-method Date of scan
runDate-methods Date of scan

-- S --

seqColors Create set of colors, interpolating through a set of preferred colors.
sequenceDesignMatrix Create design matrix for sequences
snprma Preprocessing SNP Arrays
summarize Tools for microarray preprocessing
summarize-method Tools for microarray preprocessing
summarize-methods Tools for microarray preprocessing