inmoose.deseq2.DESeqDataSet

class inmoose.deseq2.DESeqDataSet.DESeqDataSet(countData, clinicalData=None, design=None, ignoreRank=False)

DESeqDataSet extends AnnData class to store observations (samples) of variables/features in the rows of a matrix. AnnData also offers a convenient way to store observation-wise (per row) and feature-wise (per column) data.

See also

makeExampleDESeqDataSet

Methods

__init__(countData[, clinicalData, design, ...])	DESeqDataSet constructor
counts([normalized, replaced])	Accessor for the counts of a DESeqDataSet, which are stored as a matrix of non-negative integer, with one row per observation and one column per feature.
estimateDispersions([fitType, maxit, useCR, ...])	Estimate the dispersions for a DESeqDataSet
estimateSizeFactors([type_, locfunc, ...])	Estimate the size factors of a DESeqDataSet
results([contrast, name, lfcThreshold, ...])	Extract results from a DESeq() analysis
setDispFunction(value[, estimateVar])	Setter for the DESeqDataSet.dispersionFunction property

Attributes

design	design matrix
dispersions	accessor for the dispersions
dispersionFunction	dispersion function
dispersions	accessor for the dispersions
normalizationFactors	accessor for the normalization factors
sizeFactors	accessor for the size factors