This repository contains an RMarkdown document including a "complete" version with full R code to perform to identify disease-relevant Substantia nigra (SN) cell types across 33 diseases and traits with LDSCORE
This repository contains R data object and RMarkdown documents that can be used for the analysis of the datasets.
R Data objects:
- TPM expression matrix and the SN cell types identified:
Devika_midbrain.Rdata - t-statistic results generated for each gene for different cell type in the SN:
Mid_t_test.Rdata
Rmd file:
There is RMarkdown document including a "complete" version with full R code.
- Data analysis:
LDSCORE_Analysis_SN.Rmd
You will need to download here and install LDSCORE software here: https://github.com/bulik/ldsc
You will need to have the following R packages installed: biomaRt,reshape2. We will use the development versions of the Bioconductor packages.
install.packages(c("reshape2"))
## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt")
LDSCORE publication: Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types https://www.nature.com/articles/s41588-018-0081-4