CNVrd2-package | CNVrd2 |
.Random.seed | MXL population data (The 1000 Genomes Project) |
allGroups | MXL population data (The 1000 Genomes Project) |
bamFiles | MXL population data (The 1000 Genomes Project) |
calculateLDSNPandCNV | calculateLDSNPandCNV |
ccl3l1data | Data of CCL3L1 gene (The 1000 Genomes Project) |
clusteringCNVs-class | Class '"clusteringCNVs"' |
CNVrd2-class | Class '"CNVrd2"' |
copynumberGroups | MXL population data (The 1000 Genomes Project) |
countReadInWindow | Obtain read counts in constant windows. |
countReadInWindow-method | Class '"CNVrd2"' |
countReadInWindow-methods | Method 'countReadInWindow' |
emnormalCNV | Implement the EM algorithm |
emnormalCNV-method | Class '"clusteringCNVs"' |
emnormalCNV-methods | Method 'emnormalCNV' |
fcgr3bMXL | MXL population data (The 1000 Genomes Project) |
groupBayesianCNVs | groupBayesianCNVs |
groupCNVs | Cluster segmentation scores into groups. |
groupCNVs-method | Class '"clusteringCNVs"' |
groupCNVs-methods | Method 'groupCNVs' |
identifyPolymorphicRegion | Identity polymorphic regions. |
identifyPolymorphicRegion-method | Methods for Function 'identifyPolymorphicRegion' |
identifyPolymorphicRegion-methods | Methods for Function 'identifyPolymorphicRegion' |
numericOrNULL-class | Class '"numericOrNULL"' |
objectCluster | Class '"clusteringCNVs"' |
objectCNVrd2 | MXL population data (The 1000 Genomes Project) |
plotCNVrd2 | Plot traces of samples. |
plotCNVrd2-method | Class '"CNVrd2"' |
plotCNVrd2-methods | Method 'plotCNVrd2' |
plotPolymorphicRegion | Plot polymorphic regions. |
plotPolymorphicRegion-method | Methods for Function 'plotPolymorphicRegion' |
plotPolymorphicRegion-methods | Methods for Function 'plotPolymorphicRegion' |
readCountMatrix | MXL population data (The 1000 Genomes Project) |
resultSegment | MXL population data (The 1000 Genomes Project) |
searchGroupCNVs | Choose a number of CN groups |
searchGroupCNVs-method | Class '"clusteringCNVs"' |
searchGroupCNVs-methods | Method 'searchGroupCNVs' |
segmentSamples | Implement the segmentation process |
segmentSamples-method | Method 'segmentSamples' |
segmentSamples-methods | Method 'segmentSamples' |
segmentSamplesUsingPopInformation | Implement the segmentation process for multiple populations |
segmentSamplesUsingPopInformation-method | Method 'segmentSamplesUsingPopInformation' |
segmentSamplesUsingPopInformation-methods | Method 'segmentSamplesUsingPopInformation' |
vectorORfactor-class | Class '"vectorORfactor"' |