README.md

In bmskinner/tessera: Model The Effect Of Aneuploidy On Embryo Biopsies

Tessera

Tessera is a tool to visualise the impact of aneuploidy on embryo biopsies in pre-implantation genetic testing.

It includes a Shiny app that can be run from base R or RStudio.

Install

install.packages("devtools")
devtools::install_github("bmskinner/tessera")

Run the web app

The Shiny app is available at reproduction.essex.ac.uk, and is also included in the package for you to run locally if you prefer:

library(tessera)
runTessera()

The parameters

• number of cells: the size of the embryo
• proportion: the proportion of cells in the embryo that are aneuploid. Values between 0 - 1.
• dispersal: low dispersal means the aneuploid cells are clumped, high means they are scattered. Values between 0 - 1.

• number of samples: the number of cells in a single biopsy

• model all chromosomes: if selected, 23 chromosome pairs will be modelled separately, rather than a single assessment of whether the cell is aneuploid. This also reveals two new controls in the ui, detailed below.

• concordance: if concordance is 1, all chromosomes will be aneuploid in the same cells. The lower the concordance, the more chance cells will differ in which chromosomes are aneuploid. Values between 0 - 1.
• chromosome to view: choose which chromosome to display in the chart, or set as 0 to see the overall number of aneuploid chromosomes in each cell.

Compute values yourself

If you want to run simulations computationally, you can create embryos using the Embryo function with desired parameters, and count the number of aneuploid cells in all possible biopsies with the takeAllBiopsies function:

e <- Embryo(n.cells = 200, 
            n.chr   = 23,
            prop.aneuploid = 0.2,
            dispersal = 0.1,
            concordance = 1)

takeAllBiopsies(e, chromosome = 1, biopsy.size = 5)
# Output is a vector of the number of aneuploid cells from all possible biopsies

Note that since prop.aneuploid and dispersal are vectors, you can give each chromosome a different value if you wish.

bmskinner/tessera documentation built on Aug. 26, 2023, 6:46 p.m.