scCoGAPS {CoGAPS} | R Documentation

## scCoGAPS

### Description

scCoGAPS

### Usage

    scCoGAPS(simulationName, nFactor, nCores = NA, cut = NA, minNS = NA,
      manualMatch = FALSE, consensusAs = NULL, ...)

### Arguments

`simulationName` | name of this simulation
`nFactor` | number of patterns (basis vectors, metagenes), which must be greater than or equal to the number of rows of FP
`nCores` | number of cores for parallelization. If left to the default NA, nCores = nSets.
`cut` | number of branches at which to cut dendrogram used in patternMatch4singleCell
`minNS` | minimum of individual set contributions a cluster must contain
`manualMatch` | logical indicating whether or not to stop after initial phase for manual pattern matching
`consensusAs` | fixed pattern matrix to be used to ensure reciprocity of A weights accross sets
`...` | additional parameters to be fed into `gapsRun` and `gapsMapRun`

### Details

calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix for whole genome data;

### Value

list of A and P estimates

[Package CoGAPS version 3.0.2 Index]