# Single Cell Ecological Taxonomic Analysis

## Documentation for package ‘SETA’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

SETA-package | Single Cell Ecological Taxonomic Analysis
data | Synthetic single-cell, mixture and marker data
makeTypeHierarchy | Synthetic single-cell, mixture and marker data
mockCount | Synthetic single-cell, mixture and marker data
mockLong | Synthetic single-cell, mixture and marker data
mockSCE | Synthetic single-cell, mixture and marker data
mockSeurat | Synthetic single-cell, mixture and marker data
resolveGroup | 'resolveGroup()' converts a user supplied *group specification* into the column indices of the corresponding leaves in a **counts** taxa matrix. A group specification can be:
SETA | Single Cell Ecological Taxonomic Analysis
setaALR | Additive Log-Ratio (ALR) Transform
setaBalance | User-defined balance transform (geometric-mean log-ratio)
setaCLR | Centered Log-Ratio (CLR) Transform Applies a CLR transform to a matrix of counts. Samples should be in rows and taxa (cell types) in columns. For each sample, the transform computes \mathrm{CLR}(x)_i = \log \big( (x_i + c) / g(x + c) \big), where g(x + c) is the geometric mean of the row.
setaCounts | Extract Taxonomic Counts from Various Single Cell Objects
setaDistances | Compute Distance Matrix between Samples
setaILR | Isometric Log-Ratio (ILR) Transform Applies the ILR transform to an integer counts matrix. For each sample (row), the data are log-transformed (with an optional Box Cox like transformation) then projected onto an orthonormal Helmert basis, reducing dimensionality by one.
setaLatent | Compute a Latent Space from Transformed Counts
setaLogCPM | log2(CPM) Transform Computes the log2 counts-per-million (CPM) for each sample. Samples are in rows and taxa in columns.
setaMetadata | Extract Sample-Level Metadata from Various Objects
setaPercent | Percentage Transform Converts each row (sample) of a counts matrix to percentages of its row sum.
setaTaxonomyDF | Build a taxonomy data frame at multiple resolutions
setaTransform | Wrapper for Compositional Transforms with Optional Within-Lineage Resolutions A convenience function that dispatches to one of the transforms: CLR, ALR, ILR, percent, or logCPM. Note that the input 'counts' matrix should have rows as samples and columns as taxa. Optionally, you can supply a taxonomy data frame to perform a within-lineage transform at a specified resolution.
taxonomy_to_tbl_graph | Convert Multi-Column Taxonomy to a Single-Root tbl_graph (with node metadata)