B C D E F G I L M N P R S T U W misc
genoset-package | GenoSet: An eSet for data with genome locations |
baf | Get baf data |
baf-method | Get baf data |
baf2mbaf | Calculate mBAF from BAF |
baf<- | Get baf data |
baf<--method | Get baf data |
BAFSet | Create a BAFSet object |
BAFSet-class | Class '"BAFSet"' |
BAFSet-defunct | Create a BAFSet object |
BAFSet.to.ExpressionSets | Make a pair of ExpressionSets from a BAFSet |
BAFSet.to.ExpressionSets-defunct | Make a pair of ExpressionSets from a BAFSet |
boundingIndices | Find indices of features bounding a set of chromosome ranges/genes |
boundingIndices2 | Find indices of features bounding a set of chromosome ranges/genes |
boundingIndicesByChr | Find indices of features bounding a set of chromosome ranges/genes, across chromosomes |
bounds2Rle | Convert bounding indices into a Rle |
calcGC | Calculate GC Percentage in windows |
chr | Look up chromosome for each feature |
chr-method | Look up chromosome for each feature |
chrIndices | Get a matrix of first and last index of features in each chromosome |
chrIndices-method | Get a matrix of first and last index of features in each chromosome |
chrInfo | Chromosome Information |
chrInfo-method | Chromosome Information |
chrNames | Get list of unique chromosome names |
chrNames-method | Get list of unique chromosome names |
chrNames<- | Get list of unique chromosome names |
chrNames<--method | Get list of unique chromosome names |
chrOrder | Order chromosome names in proper genome order |
cn | Get or Set the cn assayData slot |
cn-method | Get or Set the cn assayData slot |
cn2lr | Take vector or matrix of copynumber values, convert to log2ratios Utility function for converting copynumber units (2 is normal) to log2ratio units (two is normal) |
cn<- | Get or Set the cn assayData slot |
cn<--method | Get or Set the cn assayData slot |
CNSet | Create a CNSet object |
CNSet-class | Class '"CNSet"' |
CNSet-defunct | Create a CNSet object |
colMeans | Means of columns |
colMeans-method | Means of columns |
colnames | Get colnames from a GenoSet |
colnames-method | Get colnames from a GenoSet |
dim | Get start of location for each feature |
dim-method | Get start of location for each feature |
elementLengths | Get start of location for each feature |
elementLengths-method | Get start of location for each feature |
end | Get start of location for each feature |
end-method | Get start of location for each feature |
fake.baf | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
fake.cn | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
fake.lrr | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
fake.pData | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
featureNames | Get rownames from RangedData, GRanges, or GenoSet |
featureNames-method | Get rownames from RangedData, GRanges, or GenoSet |
featureNames<- | Get rownames from RangedData, GRanges, or GenoSet |
featureNames<--method | Get rownames from RangedData, GRanges, or GenoSet |
fixSegNAs | Fix NA runs in a Rle |
gcCorrect | Correct copy number for GC content |
genome | Get and set the genome universe annotation. |
genome-method | Get and set the genome universe annotation. |
genome<--method | Get and set the genome universe annotation. |
genomeAxis | Label axis with base pair units |
genoPlot | Plot data along the genome |
genoPlot-method | Plot data along the genome |
genoPlot-methods | Plot data along the genome |
genoPos | Convert chromosome positions to positions from start of genome |
genoPos-method | Convert chromosome positions to positions from start of genome |
GenoSet | Create a GenoSet object |
genoset | GenoSet: An eSet for data with genome locations |
GenoSet-class | Class '"GenoSet"' |
genoset-datasets | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
genoset-defunct | Defunct genoset features |
genoset-deprecated | Deprecated genoset features |
genoset.ds | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
initGenoSet | Create a GenoSet or derivative object |
isGenomeOrder | Check if a GRanges, GenoSet or RangedData is in genome order |
isGenomeOrder-method | Check if a GRanges, GenoSet or RangedData is in genome order |
locData | Access the feature genome position info |
locData-method | Access the feature genome position info |
locData-methods | Access the feature genome position info |
locData.gr | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
locData<- | Access the feature genome position info |
locData<--method | Access the feature genome position info |
locData<--methods | Access the feature genome position info |
lr2cn | Take vector or matrix of log2 ratios, convert to copynumber Utility function for converting log2ratio units (zero is normal) to copynumber units (two is normal) |
lrr | Get lrr data |
lrr-method | Get lrr data |
lrr<- | Get lrr data |
lrr<--method | Get lrr data |
modeCenter | Center continuous data on mode |
names | Get start of location for each feature |
names-method | Get start of location for each feature |
nrow | Get start of location for each feature |
nrow-method | Get start of location for each feature |
pos | Positions for features |
pos-method | Positions for features |
rangeColMeans | Calculate column means for multiple ranges |
rangeSampleMeans | Average features in ranges per sample |
rangeSegMeanLength | Get segment widths |
rangeSegMeanLength-method | Get segment widths |
readGenoSet | Load a GenoSet from a RData file |
rownames | Get rownames from RangedData, GRanges, or GenoSet |
rownames-method | Get rownames from RangedData, GRanges, or GenoSet |
rownames<- | Get rownames from RangedData, GRanges, or GenoSet |
rownames<--method | Get rownames from RangedData, GRanges, or GenoSet |
runCBS | Run CBS Segmentation |
sampleNames | Get colnames from a GenoSet |
sampleNames-method | Get colnames from a GenoSet |
sampleNames<- | Get colnames from a GenoSet |
segPairTable | Convert Rle objects to tables of segments |
segPairTable-method | Convert Rle objects to tables of segments |
segs2Granges | GRanges from segment table |
segs2RangedData | Make a RangedData from segments |
segs2Rle | Make Rle from segments for one sample |
segs2RleDataFrame | CBS segments to probe matrix |
segTable | Convert Rle objects to tables of segments |
segTable-method | Convert Rle objects to tables of segments |
show | Show a GenoSet |
show-method | Show a GenoSet |
start | Get start of location for each feature |
start-method | Get start of location for each feature |
subsetAssayData | Subset assayData |
toGenomeOrder | Set a GRanges, GenoSet, or RangedData to genome order |
toGenomeOrder-method | Set a GRanges, GenoSet, or RangedData to genome order |
universe-method | Get and set the genome universe annotation. |
universe<--method | Get and set the genome universe annotation. |
width | Get start of location for each feature |
[ | Get start of location for each feature |
[-method | Get start of location for each feature |
[<- | Get start of location for each feature |
[<--method | Get start of location for each feature |