B C E F G I L M N O P R S U misc
baf | Get or Set the baf assayData slot... |
baf-method | Get or Set the baf assayData slot... |
baf-method | BAFSet class |
baf-methods | Get or Set the baf assayData slot... |
baf.ds | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
baf2mbaf | Calculate mBAF from BAF... |
baf<- | Get or Set the baf assayData slot... |
baf<--method | Get or Set the baf assayData slot... |
baf<--method | BAFSet class |
baf<--methods | Get or Set the baf assayData slot... |
BAFSet | Create a BAFSet object... |
BAFSet-class | BAFSet class |
bafset-class | BAFSet class |
BAFSet.to.ExpressionSets | Make a pair of ExpressionSets from a BAFSet... |
boundingIndices | Find indices of features bounding a set of chromsome ranges/genes... |
boundingIndices2 | Find indices of features bounding a set of chromsome ranges/genes... |
chr | Look up chromosome for each feature |
chr-method | Look up chromosome for each feature |
chr-method | GenoSet class |
chr-methods | 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... |
chrIndices-method | GenoSet class |
chrIndices-methods | Get a matrix of first and last index of features in each chromosome... |
chrInfo | Chromosome Information |
chrInfo-method | Chromosome Information |
chrInfo-method | GenoSet class |
chrInfo-methods | Chromosome Information |
chrOrder | Order chromosome names in proper genome order... |
class:BAFSet | BAFSet class |
class:CNSet | CNSet class |
class:GenoSet | GenoSet class |
cn | Get or Set the cn assayData slot... |
cn-method | Get or Set the cn assayData slot... |
cn-method | CNSet class |
cn-methods | Get or Set the cn assayData slot... |
cn.ds | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
cn<- | Get or Set the cn assayData slot... |
cn<--method | Get or Set the cn assayData slot... |
cn<--method | CNSet class |
cn<--methods | Get or Set the cn assayData slot... |
CNSet | Create a CNSet object... |
CNSet-class | CNSet class |
cnset-class | CNSet class |
coerce-method | BAFSet class |
coerce-method | CNSet class |
colMeans | Means of columns... |
colMeans-method | Means of columns... |
colMeans-method | GenoSet class |
colMeans-methods | Means of columns... |
elementLengths | Get space factor for GenoSet... |
elementLengths-method | GenoSet class |
elementLengths-method | Get space factor for GenoSet... |
end | Get space factor for GenoSet... |
end-method | GenoSet class |
end-method | Get space factor for GenoSet... |
fake.baf | 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<--method | GenoSet class |
gcCorrect | cgCorrect |
genomeAxis | Label axis with base pair units |
genomeOrder | Get indices to set a RangedData or GenoSet to genome order... |
genoPlot | genoPlot,-method |
genoPlot-method | BAFSet class |
genoPlot-method | CNSet class |
genoPlot-method | genoPlot,-method |
genoPlot-method | GenoSet class |
genoPlot-methods | genoPlot,-method |
genoPos | Convert chromosome positions to positions from start of genome |
genoPos-method | Convert chromosome positions to positions from start of genome |
genoPos-method | GenoSet class |
genoPos-methods | Convert chromosome positions to positions from start of genome |
GenoSet | Create a GenoSet object... |
genoset | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
GenoSet-class | GenoSet class |
genoset-class | GenoSet class |
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 RangedData or GenoSet is in genome order... |
locData | Get and set probe set info |
locData-method | GenoSet class |
locData-method | Get and set probe set info |
locData-methods | Get and set probe set info |
locData.rd | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
locData<- | Get and set probe set info |
locData<--method | GenoSet class |
locData<--method | Get and set probe set info |
lrr | Get or Set the lrr assayData slot... |
lrr-method | BAFSet class |
lrr-method | Get or Set the lrr assayData slot... |
lrr-methods | Get or Set the lrr assayData slot... |
lrr<- | Get or Set the lrr assayData slot... |
lrr<--method | BAFSet class |
lrr<--method | Get or Set the lrr assayData slot... |
lrr<--methods | Get or Set the lrr assayData slot... |
modeCenter | Center continuous data on mode... |
names | Get space factor for GenoSet... |
names-method | GenoSet class |
names-method | Get space factor for GenoSet... |
orderedChrs | Get chromosome names in genome order... |
orderedChrs-method | GenoSet class |
orderedChrs-method | Get chromosome names in genome order... |
orderedChrs-methods | Get chromosome names in genome order... |
pos | Positions for features |
pos-method | GenoSet class |
pos-method | Positions for features |
pos-methods | Positions for features |
ranges | Get space factor for GenoSet... |
ranges-method | GenoSet class |
ranges-method | Get space factor for GenoSet... |
rangeSampleMeans | Average features in ranges per sample... |
runCBS | Run CBS Segmentation |
segment | Run CBS Segmentation |
segmentation | Run CBS Segmentation |
segs2Rle | Make Rle from segments for one sample... |
segs2RleDataFrame | CBS segments to probe matrix |
segTable | Take a DataFrame of Rle vectors and make a list of data... |
show-method | GenoSet class |
space | Get space factor for GenoSet... |
space-method | GenoSet class |
space-method | Get space factor for GenoSet... |
start | Get space factor for GenoSet... |
start-method | GenoSet class |
start-method | Get space factor for GenoSet... |
subsetAssayData | Subset assayData |
uniqueChrs | Get list of unique chromosome names... |
uniqueChrs-method | GenoSet class |
uniqueChrs-method | Get list of unique chromosome names... |
uniqueChrs-methods | Get list of unique chromosome names... |
universe | Get and set the genome universe annotation. |
universe-method | GenoSet class |
universe-method | Get and set the genome universe annotation. |
universe<- | Get and set the genome universe annotation. |
universe<--method | GenoSet class |
universe<--method | Get and set the genome universe annotation. |
[ | Get space factor for GenoSet... |
[-method | GenoSet class |
[-method | Get space factor for GenoSet... |
[[ | Get space factor for GenoSet... |
[[-method | Get space factor for GenoSet... |