NBumiCheckFit {M3Drop} | R Documentation

## Check Fit Quality

### Description

Checks the quality of the fit of the depth-adjusted negative binomial model.

### Usage

    	NBumiCheckFit(counts, fit, suppress.plot=FALSE)
    	NBumiCheckFitFS(counts, fit, suppress.plot=FALSE)

### Arguments

`counts` | a numeric matrix of raw UMI counts, columns = samples, rows = genes.
`fit` | output from NBumiFitModel or NBumiFitBasicModel.
`suppress.plot` | Whether to plot the observed vs expected frequency of dropouts for genes & cells.

### Details

Calculates expected dropouts for genes and cells and compares to observed values. Optionally plots observed vs expected dropouts for both genes and cells. `NBumiCheckFit` uses depth-adjusted negative binomial with gene-specific dispersions. `NBumiCheckFitFS` uses depth-adjusted negative binomial with dispersions calculated from the power-law between gene-specific dispersion and mean expression (as is used for feature selection).

### Value

Invisibly, named list of output: gene_error = sum of squared error between observed and expected gene-specific total dropouts cell_error = sum of squared error between observed and expected cell-specific total dropouts exp_ps = gene by sample matrix of probability of a dropout for the negative binomial model fitted to each observation.

### Examples

    	library(M3DExampleData)
    	counts <- NBumiConvertData(Mmus_example_list$data)
    	fit <- NBumiFitModel(counts);
    	fit_quality <- NBumiCheckFitFS(counts, fit);

[Package M3Drop version 1.12.0 Index]