# The 'reads' data.frame or
# RangedSummarizedExperiment object should
# have row and column names that are unique,
# and looks like the following:
#
# T1a T1b T2 T3 N1 N2 Nx
# Gene_00001 0 0 2 0 0 1 0
# Gene_00002 20 8 12 5 19 26 14
# Gene_00003 3 0 2 0 0 0 1
# Gene_00004 75 84 241 149 271 257 188
# Gene_00005 10 16 4 0 4 10 10
# Gene_00006 129 126 451 223 243 149 209
# ... many more rows ...
data(selex)
# x is an object of type aldex.clr
x <- aldex.clr(selex, mc.samples = 2, verbose = FALSE)
# get all of the Monte Carlo Dirochlet instances
monteCarloInstances <- getMonteCarloInstances(x)
# get sample names
sampleIDs <- getSampleIDs(x)
# get features
features <- getFeatures(x)
# get number of features
numFeatures <- numFeatures(x)
# get number of Monte Carlo Dirochlet instances
numInstances <- numMCInstances(x)
# get names of features
featureNames <- getFeatureNames(x)
# get number of conditions
conditions <- numConditions(x)
# get number of conditions
reads <- getReads(x)
# retrieve the first Monte Carlo Dirochlet instance.
monteCarloInstance <- getMonteCarloReplicate(x,1)
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