Preprocessing tools for oligonucleotide arrays.


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Documentation for package ‘oligo’ version 1.12.2

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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 arrays

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

-- 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