prepareObserved {benchdamic} | R Documentation

## prepareObserved

### Description

Continuity corrected logarithms of the average counts and fraction of zeroes by feature.

### Usage

    prepareObserved(counts, scale = NULL)

### Arguments

`counts` | a phyloseq object or a matrix of counts with features (OTUs, ASVs, genes) by row and samples by column.
`scale` | If specified it refers to the character vector used in `fitHURDLE` function. Either `median` or `default` to choose between the median library size or one million as scaling factors for raw counts.

### Value

A data frame containing the continuity corrected logarithm for the raw count mean values for each taxon of the matrix of counts in the `Y` column and the observed zero rate in the `Y0` column. If `scale` is specified the continuity corrected logarithm for the mean CPM (`scale = "default"`) or the mean counts per median library size (`scale = "median"`) is computed instead.

### See Also

`meanDifferences`

### Examples

    # Generate some random counts
    counts <- matrix(rnbinom(n = 60, size = 3, prob = 0.5), nrow = 10, ncol = 6)

    observed1 <- prepareObserved(counts)
    # For the comparison with HURDLE model
    observed2 <- prepareObserved(counts, scale = "median")

[Package benchdamic version 1.0.0 Index]