> ## Documentation Index
> Fetch the complete documentation index at: https://mintlify.com/satijalab/seurat-wrappers/llms.txt
> Use this file to discover all available pages before exploring further.

# RunCoGAPS()

> Bayesian non-negative matrix factorization for pattern discovery in single-cell data

`RunCoGAPS()` runs the CoGAPS (Coordinated Gene Activity in Pattern Sets) algorithm on a Seurat object. It decomposes the expression matrix into latent patterns via sparse Bayesian NMF, storing results as a DimReduc object.

## Syntax

```r theme={null}
RunCoGAPS(
  object,
  assay = NULL,
  slot = "counts",
  params = NULL,
  temp.file = NULL,
  reduction.name = "CoGAPS",
  reduction.key = "CoGAPS_",
  ...
)
```

## Parameters

<ParamField path="object" type="Seurat" required>
  A Seurat object.
</ParamField>

<ParamField path="assay" type="character" default="NULL">
  Assay to pull expression data from. Defaults to the active default assay.
</ParamField>

<ParamField path="slot" type="character" default="counts">
  Slot within the assay to use. Data is log2-transformed (`log2(x + 1)`) internally before being passed to CoGAPS.
</ParamField>

<ParamField path="params" type="CogapsParams" default="NULL">
  A `CogapsParams` object specifying CoGAPS settings such as `nPatterns`, `nIterations`, `singleCell`, `sparseOptimization`, and distributed mode. If `NULL`, CoGAPS runs with default parameters.
</ParamField>

<ParamField path="temp.file" type="character or logical" default="NULL">
  If `TRUE`, creates a temporary `.mtx` file for the data matrix (required for distributed CoGAPS). If a string, uses that path as the temporary file. Leave `NULL` for in-memory execution.
</ParamField>

<ParamField path="reduction.name" type="character" default="CoGAPS">
  Name for the resulting DimReduc object stored in the Seurat object.
</ParamField>

<ParamField path="reduction.key" type="character" default="CoGAPS_">
  Column name prefix for the CoGAPS embedding dimensions.
</ParamField>

<ParamField path="..." type="any">
  Additional parameters passed to `CoGAPS::CoGAPS()`.
</ParamField>

## Returns

A Seurat object with a new DimReduc object stored under `reduction.name`. Cell embeddings correspond to `sampleFactors` and feature loadings correspond to `featureLoadings` from the CoGAPS result.

## Examples

```r theme={null}
library(SeuratWrappers)
BiocManager::install("CoGAPS")

# Basic run with default parameters
object <- RunCoGAPS(object = seurat_obj)

# Specify number of patterns and iterations
params <- CoGAPS::CogapsParams()
params <- CoGAPS::setParam(params, "nPatterns", 8)
params <- CoGAPS::setParam(params, "nIterations", 50000)
object <- RunCoGAPS(object = seurat_obj, params = params)

# Visualize patterns
VlnPlot(object, features = paste0("CoGAPS_", 1:8), group.by = "seurat_clusters")
```

## See Also

* [CoGAPS method guide](/methods/cogaps)