Man pages for benilton/oligoOld
Preprocessing tools for oligonucleotide arrays

basecontentSequence Base Contents
basicPLMSimplified interface to PLM.
basicRMASimplified interface to RMA.
chromosomeAccessor for chromosome information
colorsCreate set of colors, interpolating through a set of...
coordinatesAccessors for physical array coordinates.
crlmmGenotype Calls
fitProbeLevelModelTool to fit Probe Level Models.
getAffinitySplineCoefficientsEstimate affinity coefficients.
getBaseProfileCompute and plot nucleotide profile.
getContainerGet container information for NimbleGen Tiling Arrays.
getCrlmmSummariesFunction to get CRLMM summaries saved to disk
getNetAffxNetAffx Biological Annotations
getNgsColorsInfoHelper function to extract color information for filenames on...
getPlatformDesignRetrieve Platform Design object
getProbeInfoProbe information selector.
histDensity estimate
imageDisplay a pseudo-image of a microarray chip
Index-methodsAccessors for PM, MM or background probes indices.
IntensityMatrix-methodsAccessors and replacement methods for the intensity/PM/MM/BG...
justSNPRMASummarization of SNP data
list.xysfilesList XYS files
MAplot-methodsMA plots
oligoDefunctDefunct Functions in Package 'oligo'
oligo-packageThe oligo package: a tool for low-level analysis of...
oligoPLM-classClass '"oligoPLM"'
paCallsMethods for P/A Calls
plotM-methodsMethods for Log-Ratio plotting
pmAlleleAccess the allele information for PM probes.
pmFragmentLengthAccess the fragment length for PM probes.
pmPositionAccessor to position information
pmStrandAccessor to the strand information
preprocessToolsTools for microarray preprocessing.
probeNamesAccessor to feature names
read.celfilesParser to CEL files
readSummariesRead summaries generated by crlmm
read.xysfilesParser to XYS files
rma-methodsRMA - Robust Multichip Average algorithm
runDateDate of scan
sequenceDesignMatrixCreate design matrix for sequences
Sequences-methodsProbe Sequeces
snprmaPreprocessing SNP Arrays
benilton/oligoOld documentation built on May 12, 2019, 11:52 a.m.