extract results objects after running scDD analysis
An object of class
A character variable specifying which output is desired, with possible values "Genes", "Zhat.c1", "Zhat.c2", and "Zhat.overall". The default value is "Genes", which contains a a data frame with nine columns: gene name (matches rownames of SCdat), permutation p-value for testing of independence of condition membership with clustering, Benjamini-Hochberg adjusted version of the previous column, p-value for test of difference in dropout rate (only for non-DD genes), Benjamini-Hochberg adjusted version of the previous column, name of the DD (DE, DP, DM, DB) pattern or DZ (otherwise NS = not significant), the number of clusters identified overall, the number of clusters identified in condition 1 alone, and the number of clusters identified in condition 2 alone.
Convenient helper function to extract the results (gene
classifications, pvalues, and clustering information). Results
data.frames/matrices are stored in the
metadata slot and can also be accessed without the help of this
convenience function by calling
data.frame which contains either the gene classification
and p-value results, or cluster membership information, as detailed in the
description of the
type input parameter.
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# load toy simulated example SingleCellExperiment object to find DD genes data(scDatExSim) # set arguments to pass to scDD function prior_param=list(alpha=0.01, mu0=0, s0=0.01, a0=0.01, b0=0.01) # call the scDD function to perform permutations and classify DD genes scDatExSim <- scDD(scDatExSim, prior_param=prior_param, testZeroes=FALSE) # extract main results object RES <- results(scDatExSim)
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