Package index • GenomicDataStream

GenomicDataStream

GenomicDataStream(): GenomicDataStream
GenomicDataStream-class: Interface to genomic data files
getNextChunk(): Get data chunk from GenomicDataStream
initializeStream(): Initialize GenomicDataStream
setChunkSize(): Set Chunk Size
setRegion(): Set regions of GenomicDataStream

Out-of-core SVD

dashSVD(): Dynamic Shifts Based Randomized SVD
PCAone(): Window-based Randomized SVD with PCAone
PCA-class: PCA result

Accessor functions

atEndOfStream(): Detected if end of stream is reached
countChunks(): Get chunk sizes
featuresRead(): Get number of features read from GenomicDataStream
getSampleNames(): Get sample names
getVariantLocations(): Get location of each feature
isInitialized(): Get status of GenomicDataStream
plot(<PCA>,<ANY>): Plot PCAone
print(<GenomicDataStream>) print(<PCA>): Print object
rownames(<GenomicDataStream>): Get rownames
show(<GenomicDataStream>) show(<PCA>): Show object
getChromRanges(): Get ranges for each chromosome
chopChroms(): Get genomic intervals
summarizeChunks(): Get information about chunks

Other functions

standardize_in_place(): Standardize matrix columns in place
normPC(): Normalize principal components
perfMetric(): Evaluate performance of PC estimates
readH5AD(): Read H5AD as SingleCellExperiment