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]