Wrapper function for the branch cell selection parameters

Parameters controlling which cells run_gene_trends_sc() assigns to each branch. The threshold on a fate's probability is an expanding quantile over the pseudotime-sorted cells, made monotone with a cumulative maximum, so a fate's bar can only rise as differentiation proceeds. The defaults are the reference ones.

Usage

params_sc_branch_selection(q = 0.01, eps = 0.01, resolution = 500L)

Arguments

q

Numeric. Upper-tail quantile of the fate probability used as the threshold. Defaults to 0.01.

eps

Numeric. Slack subtracted from the threshold before the comparison. Defaults to 0.01.

resolution

Integer. Number of pseudotime buckets, capped at the cell count. Defaults to 500L.

Value

A named list with the following elements:

• q - Numeric. Upper-tail quantile of the fate probability used as the threshold. Defaults to 0.01.

• eps - Numeric. Slack subtracted from the threshold before the comparison. Defaults to 0.01.

• resolution - Integer. Number of pseudotime buckets, capped at the cell count. Defaults to 500L.

References

Setty, et al., Nat. Biotechnol., 2019.