R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 71 found.
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BAFfromClusterMeans (Package: GWASTools) : B Allele Frequency & Log R Ratio Calculation

This function calculates the B allele frequency and the log R ratio values from the mean R and theta values for each cluster.

● Data Source: BioConductor
● Keywords: datagen, manip
● Alias: BAFfromClusterMeans
● 0 images

BAFfromGenotypes (Package: GWASTools) : B Allele Frequency & Log R Ratio Calculation

This function calculates the B allele frequency and the log R ratio values for samples by either plate or by study.

● Data Source: BioConductor
● Keywords: datagen, manip
● Alias: BAFfromGenotypes
● 0 images

GWASTools-package (Package: GWASTools) : Tools for Genome Wide Association Studies

This package contains tools for facilitating cleaning (quality control and quality assurance) and analysis of GWAS data.

● Data Source: BioConductor
● Keywords: package
● Alias: GWASTools, GWASTools-package
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GdsGenotypeReader (Package: GWASTools) : Class GdsGenotypeReader

The GdsGenotypeReader class is an extension of the GdsReader class specific to reading genotype data stored in GDS files. GDS files with both snp x scan and scan x snp dimensions are supported.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: GdsGenotypeReader, GdsGenotypeReader-class, MchromCode,GdsGenotypeReader-method, XYchromCode,GdsGenotypeReader-method, XchromCode,GdsGenotypeReader-method, YchromCode,GdsGenotypeReader-method, autosomeCode,GdsGenotypeReader-method, getAlleleA,GdsGenotypeReader-method, getAlleleB,GdsGenotypeReader-method, getChromosome,GdsGenotypeReader-method, getGenotype,GdsGenotypeReader-method, getGenotypeSelection,GdsGenotypeReader-method, getPosition,GdsGenotypeReader-method, getScanID,GdsGenotypeReader-method, getSnpID,GdsGenotypeReader-method, getVariable,GdsGenotypeReader-method, nscan,GdsGenotypeReader-method, nsnp,GdsGenotypeReader-method
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GdsIntensityReader (Package: GWASTools) : Class GdsIntensityReader

The GdsIntensityReader class is an extension of the GdsReader class specific to reading intensity data stored in GDS files.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: GdsIntensityReader, GdsIntensityReader-class, MchromCode,GdsIntensityReader-method, XYchromCode,GdsIntensityReader-method, XchromCode,GdsIntensityReader-method, YchromCode,GdsIntensityReader-method, autosomeCode,GdsIntensityReader-method, getBAlleleFreq,GdsIntensityReader-method, getChromosome,GdsIntensityReader-method, getLogRRatio,GdsIntensityReader-method, getPosition,GdsIntensityReader-method, getQuality,GdsIntensityReader-method, getScanID,GdsIntensityReader-method, getSnpID,GdsIntensityReader-method, getVariable,GdsIntensityReader-method, getX,GdsIntensityReader-method, getY,GdsIntensityReader-method, hasBAlleleFreq,GdsIntensityReader-method, hasLogRRatio,GdsIntensityReader-method, hasQuality,GdsIntensityReader-method, hasX,GdsIntensityReader-method, hasY,GdsIntensityReader-method, nscan,GdsIntensityReader-method, nsnp,GdsIntensityReader-method
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GdsReader (Package: GWASTools) : Class GdsReader

The GdsReader class provides an interface for reading GDS files.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: GdsReader, GdsReader-class, close,GdsReader-method, getAttribute,GdsReader-method, getDimension,GdsReader-method, getNodeDescription,GdsReader-method, getVariable,GdsReader-method, getVariableNames,GdsReader-method, hasVariable,GdsReader-method, open,GdsReader-method, show,GdsReader-method
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GenotypeData-class (Package: GWASTools) : Class GenotypeData

The GenotypeData class is a container for storing genotype data from a genome-wide association study together with the metadata associated with the subjects and SNPs involved in the study.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: GenotypeData, GenotypeData-class, MchromCode,GenotypeData-method, XYchromCode,GenotypeData-method, XchromCode,GenotypeData-method, YchromCode,GenotypeData-method, autosomeCode,GenotypeData-method, close,GenotypeData-method, getAlleleA,GenotypeData-method, getAlleleB,GenotypeData-method, getChromosome,GenotypeData-method, getGenotype,GenotypeData-method, getGenotypeSelection,GenotypeData-method, getPosition,GenotypeData-method, getScanAnnotation,GenotypeData-method, getScanID,GenotypeData-method, getScanVariable,GenotypeData-method, getScanVariableNames,GenotypeData-method, getSex,GenotypeData-method, getSnpAnnotation,GenotypeData-method, getSnpID,GenotypeData-method, getSnpVariable,GenotypeData-method, getSnpVariableNames,GenotypeData-method, getVariable,GenotypeData-method, hasScanAnnotation,GenotypeData-method, hasScanVariable,GenotypeData-method, hasSex,GenotypeData-method, hasSnpAnnotation,GenotypeData-method, hasSnpVariable,GenotypeData-method, hasVariable,GenotypeData-method, nscan,GenotypeData-method, nsnp,GenotypeData-method, open,GenotypeData-method, show,GenotypeData-method
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IntensityData-class (Package: GWASTools) : Class IntensityData

The IntensityData class is a container for storing intensity data from a genome-wide association study together with the metadata associated with the subjects and SNPs involved in the study.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: IntensityData, IntensityData-class, MchromCode,IntensityData-method, XYchromCode,IntensityData-method, XchromCode,IntensityData-method, YchromCode,IntensityData-method, autosomeCode,IntensityData-method, close,IntensityData-method, getBAlleleFreq,IntensityData-method, getChromosome,IntensityData-method, getLogRRatio,IntensityData-method, getPosition,IntensityData-method, getQuality,IntensityData-method, getScanID,IntensityData-method, getScanVariable,IntensityData-method, getScanVariableNames,IntensityData-method, getSex,IntensityData-method, getSnpID,IntensityData-method, getSnpVariable,IntensityData-method, getSnpVariableNames,IntensityData-method, getVariable,IntensityData-method, getX,IntensityData-method, getY,IntensityData-method, hasBAlleleFreq,IntensityData-method, hasLogRRatio,IntensityData-method, hasQuality,IntensityData-method, hasScanAnnotation,IntensityData-method, hasScanVariable,IntensityData-method, hasSex,IntensityData-method, hasSnpAnnotation,IntensityData-method, hasSnpVariable,IntensityData-method, hasVariable,IntensityData-method, hasX,IntensityData-method, hasY,IntensityData-method, nscan,IntensityData-method, nsnp,IntensityData-method, open,IntensityData-method, show,IntensityData-method
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MatrixGenotypeReader (Package: GWASTools) : Class MatrixGenotypeReader

The MatrixGenotypeReader class stores a matrix of genotypes as well as SNP and scan IDs, chromosome, and position.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: MatrixGenotypeReader, MatrixGenotypeReader-class, MchromCode,MatrixGenotypeReader-method, XYchromCode,MatrixGenotypeReader-method, XchromCode,MatrixGenotypeReader-method, YchromCode,MatrixGenotypeReader-method, autosomeCode,MatrixGenotypeReader-method, getChromosome,MatrixGenotypeReader-method, getGenotype,MatrixGenotypeReader-method, getGenotypeSelection,MatrixGenotypeReader-method, getPosition,MatrixGenotypeReader-method, getScanID,MatrixGenotypeReader-method, getSnpID,MatrixGenotypeReader-method, nscan,MatrixGenotypeReader-method, nsnp,MatrixGenotypeReader-method, show,MatrixGenotypeReader-method
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NcdfGenotypeReader (Package: GWASTools) : Class NcdfGenotypeReader

The NcdfGenotypeReader class is an extension of the NcdfReader class specific to reading genotype data stored in NetCDF files.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: MchromCode,NcdfGenotypeReader-method, NcdfGenotypeReader, NcdfGenotypeReader-class, XYchromCode,NcdfGenotypeReader-method, XchromCode,NcdfGenotypeReader-method, YchromCode,NcdfGenotypeReader-method, autosomeCode,NcdfGenotypeReader-method, getChromosome,NcdfGenotypeReader-method, getGenotype,NcdfGenotypeReader-method, getPosition,NcdfGenotypeReader-method, getScanID,NcdfGenotypeReader-method, getSnpID,NcdfGenotypeReader-method, getVariable,NcdfGenotypeReader-method, nscan,NcdfGenotypeReader-method, nsnp,NcdfGenotypeReader-method
● 0 images