Integration Gene Set Analysis for SNP.
intGSASNP is an R package that contains the implementation of six algorithms (ORA, CERNO, MAGENTA, GSEA, iGSEA4GWAS, and GSEA-SNP) selected for studying the importance importance of SNP integration for gene set analysis in GWAS. Features that distinguish intGSASNP include:
- selection of preferred integration method (minimum p-value method, Fisher's method, Stouffer's method) and permutation method (by Entrez, SNP, or raw SNP),
- possible application of correction for multiple testing,
- option to choose the number of permutations,
- option to apply LD correction.
Additionally, an example of a dataset with sample refSNP ids, entrez ids, and p-values is provided.
You can install the package from GitHub with:
# install.packages("devtools")
devtools::install_github("ZAEDPolSl/intGSASNP")Documentation can be accessed using:
library(intGSASNP)