inmoose.deseq2.DESeqDataSet.DESeqDataSet.__init__

DESeqDataSet.__init__(countData, clinicalData=None, design=None, ignoreRank=False)

DESeqDataSet constructor

Parameters:

  • countData (pandas.DataFrame or DESeqDataSet) – Raw counts (if pandas.DataFrame) or DESeqDataSet object to copy. Raw counts matrix has one column per feature (usually genes) and one row per observation (usually single cells or samples).

  • clinicalData (pandas.DataFrame) – Observation-wise clinical data. Arbitrary number of columns, as many rows as in countData.

  • design (patsy.DesignMatrix-like) – An object (formula, matrix…) representing the design matrix. It will be fed to patsy.dmatrix and the resulting patsy.DesignMatrix will be stored in the DESeqDataSet.

  • ignoreRank (bool, optional) – Whether to ignore testing that the design matrix is full rank.