foldchanger

foldchanger is a package for performing fold change calculations.

These calculations are used for the detection of genetic copy number variants by next generation sequencing. I am building foldchanger as a mini-project to teach myself R package development.

Installation

You can install the development version of foldchanger from GitHub with:

# install.packages("pak")
pak::pak("joe-m-shaw/foldchanger")

Usage

foldchanger provides a bunch of helpful functions to make interacting with fold changes and log2ratios easier.

For example, pred_cpc can be used to predict the copies per cell (CPC) of genes within a tumour sample, based on neoplastic cell content (NCC) and fold change.

Let’s imagine you measure a fold change of 11 for the EGFR gene in a tumour sample with an NCC of 65%:

library(foldchanger)
pred_cpc(fc = 11, ncc = 65, dir = "gain")
#> [1] 33

Then you want to predict what fold change you would see if you had a sample with 109 copies of EGFR per tumour cell and an NCC of 26%:

pred_fc(tumour_cpc = 109, ncc = 26, dir = "gain")
#> [1] 14.9

Or you want to change between the two forms of fold change and log2ratio:

change(1, from = "fcgain", to = "log2r")
#> [1] 0

change(-1, from = "log2r", to = "fcloss")
#> [1] -2