escoSimTreeDE: Simulate differential expression (DE) factors for tree...
In JINJINT/splattermodify: Simple Simulation of Single-cell RNA Sequencing Data

Description Usage Arguments Details Value References

DE factors for each tree branches are produced using getLNormFactors with means follows a multivariate normal ditribution, where the correlation relationship is generated from the tree structure.

1	escoSimTreeDE(sim, verbose)

`sim`	SingleCellExperiment to add differential expression to.
`verbose`	logical. Whether to print progress messages

The method of simulating paths is inspired by the method used in SymSim simulation. Particularly, the tree structure is generated by making the DE factors more similar for closer tree branches, and less similar for far away tree branches. The tree structure is input through tree in object escoParams, and we generate the relationship between DE factors for different branches from the estimated evolutionary variance-covariance matrix of the tree using vcv.phylo.

SingleCellExperiment with simulated differential expression.

Zhang, X., Xu, C. & Yosef, N. Simulating multiple faceted variability in single cell RNA sequencing. Nat Commun 10, 2611 (2019). https://doi.org/10.1038/s41467-019-10500-w.

JINJINT/splattermodify documentation built on May 19, 2021, 4:05 p.m.