Description Usage Arguments Details Value Examples

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

1 2 | ```
NBumiCheckFit(counts, fit, suppress.plot=FALSE)
NBumiCheckFitFS(counts, fit, suppress.plot=FALSE)
``` |

`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. |

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).

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.

1 2 3 4 | ```
library(M3DExampleData)
counts <- NBumiConvertData(Mmus_example_list$data)
fit <- NBumiFitModel(counts);
fit_quality <- NBumiCheckFitFS(counts, fit);
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.