Description Usage Arguments Details Value References Examples

Default function to calculate the negative binomial dispersion parameter given the mean expression of the gene.

1 | ```
bg__default_mean2disp(mu, coeffs=c(3.967816,-1.855054))
``` |

`mu` |
mean expression of the gene(s) |

`coeffs` |
coefficients of linear regression between log(cv2) and log10(mean expression) for observed data. |

Given the coefficients of a linear regression between the natural logarithm of the squared coefficient of variation and log base 10 of mean expression, calculates the dispersion parameter (1/size) of the negative binomial distribution for a given expression level.

Default coefficients were fit to the Buettner at al.[1] single cell mESC data.

the dispersion parameter (1/size) for the (mu,size) paramterization of the `rnbinom`

function.

[1] Buettner et al. (2015) Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature Biotechnology 33 : 155-160.

1 2 3 4 | ```
# mu <- 100
# r <- bg__default_mean2disp(mu)
# n_cells <- 50
# sim <- rnbinom(n_cells, size=1/r, mu=mu)
``` |

tallulandrews/M3D documentation built on May 31, 2019, 2:55 a.m.

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