Package index • GenomicDataStream

Core functions

GenomicDataStream(): GenomicDataStream

GenomicDataStream-class: Interface to genomic data files

PCAstream(): Window-based Randomized SVD

PCA-class: PCA result

Interact with stream

getNextChunk(): Get data chunk from GenomicDataStream

initializeStream(): Initialize GenomicDataStream

setChunkSize(): Set Chunk Size

setRegion(): Set regions of GenomicDataStream

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 PCAstream

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