genoset-package |
GenoSet: An eSet for data with genome locations |
baf2mbaf |
Calculate mBAF from BAF |
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 |
Chromosome name for each feature |
chr-method |
Chromosome name 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 |
Get chromosome start and stop positions |
chrInfo-method |
Get chromosome start and stop positions |
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 |
cn2lr |
Take vector or matrix of copynumber values, convert to log2ratios |
cn2lr-method |
Take vector or matrix of copynumber values, convert to log2ratios |
colMeans |
Means of columns |
colMeans-method |
Means of columns |
colnames-method |
Get colnames from a GenoSet |
colnames<--method |
Get colnames from a GenoSet |
dim-method |
Dimensions |
elementLengths-method |
Get elementLengths from locData slot |
end-method |
Get end 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-method |
Get rownames from GRanges, or GenoSet |
featureNames<--method |
Get rownames from 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 |
Genome version |
genomeAxis |
Label axis with base pair units |
genoPlot |
Plot data along the genome |
genoPlot-method |
Plot data along the genome |
genoPos |
Get base positions of features in genome-scale units |
genoPos-method |
Get base positions of features in genome-scale units |
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. |
GenoSetOrGenomicRanges-class |
Class '"GenoSet"' |
initGenoSet |
Create a GenoSet or derivative object |
isGenomeOrder |
Check if a GRanges orGenoSet is in genome order |
isGenomeOrder-method |
Check if a GRanges orGenoSet is in genome order |
locData |
Access the feature genome position info |
locData-method |
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 |
lr2cn |
Take vector or matrix of log2 ratios, convert to copynumber |
modeCenter |
Center continuous data on mode |
names-method |
Get data matrix names |
nrow-method |
Number of rows |
pos |
Chromosome position of features |
pos-method |
Chromosome position of features |
rangeColMeans |
Calculate column means for multiple ranges |
RangedDataOrGenomicRanges-class |
Class '"GenoSet"' |
RangedDataOrGenoset-class |
Class '"GenoSet"' |
RangedDataOrGenoSetOrGenomicRanges-class |
Class '"GenoSet"' |
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-method |
Get rownames from GRanges, or GenoSet |
rownames<--method |
Get rownames from GRanges, or GenoSet |
runCBS |
Run CBS Segmentation |
sampleNames-method |
Get colnames from a GenoSet |
sampleNames<--method |
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-method |
Print a GenoSet |
start-method |
Get start of location for each feature |
subsetAssayData |
Subset or re-order assayData |
toGenomeOrder |
Set a GRanges or GenoSet to genome order |
toGenomeOrder-method |
Set a GRanges or GenoSet to genome order |
universe-method |
Get universe annotations |
universe<--method |
Get universe annotations |
width-method |
Get width of location for each feature |
[-method |
Subset a GenoSet |
[<--method |
Subset a GenoSet |