aldex.clr-class {ALDEx2} | R Documentation

## The aldex.clr class

### Description

The aldex.clr S4 class is a class which stores the data generated by the aldex.clr method.

### Details

An aldex.clr object contains the Monte Carlo Dirochlet instances derived from estimating the technical variance of the raw read count data. It is created by the `aldex.clr.function`, which is invoked by the aldex.clr method. It consists of four attributes: the sample names, the feature names, the conditions vector (assigns each sample to a condition), and the Monte Carlo Dirochlet instances themselves. These can be accessed, along with information about the length of some attributes. A single Monte Carlo instance can also be retrieved.

### Value

The aldex.clr object contains the clr transformed values for each Monte-Carlo Dirichlet instance, which can be accessed through `getMonteCarloInstances(x)`, where `x` is the `clr` function output. Each list element is named by the sample ID. `getFeatures(x)` returns the features, `getSampleIDs(x)` returns sample IDs, and `getFeatureNames(x)` returns the feature names.

### Methods

In the code below, `x` is an `aldex.clr` object, and `i` is a numeric whole number.

  `getMonteCarloInstances(x)`: Returns `x`'s Monte Carlo Dirichlet instances.

  `getSampleIDs(x)`: Returns the names of the samples. These can be used to access the original reads, as in `reads\$sampleID` (if the reads are a data frame).

  `getFeatures(x)`: Returns the names of the features as a vector.

  `numFeatures(x)`: Returns the number of features associated with the data.

  `numMCInstances(x)`: Returns the names of the `keys` that can be used to subset the data rows. The `keys` values are the rsid's.

  `getFeatureNames(x)`: Returns the names of the `keys` that can be used to subset the data rows. The `keys` values are the rsid's.

  `getReads(x)`: Returns the names of the `keys` that can be used to subset the data rows. The `keys` values are the rsid's.

  `numConditions(x)`: Returns the names of the `keys` that can be used to subset the data rows. The `keys` values are the rsid's.

  `getMonteCarloReplicate(x, i)`: Returns the names of the `keys` that can be used to subset the data rows. The `keys` values are the rsid's.

### Author(s)

Greg Gloor, Ruth Grace Wong, Andrew Fernandes, Jia Rong Wu and Matt Links contributed to this code

### References

Please use the citation given by `citation(package="ALDEx")`.

### See Also

`aldex.clr.function`

### Examples

        # The 'reads' data.frame or
        # SummarizedExperiment 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)
        #subset for efficiency
        selex <- selex[1201:1600,]
        conds <- c(rep("NS", 7), rep("S", 7))

        # x is an object of type aldex.clr
        x <- aldex.clr(selex, conds, mc.samples = 2, denom="all", 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)

[Package ALDEx2 version 1.18.0 Index]