spatialDmelxsim

Allelic counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object.

Package is available on Bioconductor as of August 2021:

https://bioconductor.org/packages/spatialDmelxsim

After the package is released in October 2021:

BiocManager::install("spatialDmelxsim")
suppressPackageStartupMessages(library(SummarizedExperiment))
library(spatialDmelxsim)
se <- spatialDmelxsim()

The assays of se include a1 and a2. Here, a1 assay is the D simulans allelic count, a2 assay is the D melanogaster allelic count.

Data downloaded from GSE102233 as described in the publication:

Combs PA, Fraser HB (2018) Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic. PLOS Genetics 14(11): e1007631. https://doi.org/10.1371/journal.pgen.1007631

R scripts

• Script to build the SummarizedExperiment: inst/scripts/make-data.R
• Demo of loading the data and calculating allelic ratio: vignettes/spatialDmelxsim.Rmd

Example figures of allelic ratio (simulans / total):

See vignette for details.