README.md

In ZAEDPolSl/intGSASNP: Integration Gene Set Analysis for SNP

intGSASNP

Integration Gene Set Analysis for SNP.

Description

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.

Installation

You can install the package from GitHub with:

# install.packages("devtools")
devtools::install_github("ZAEDPolSl/intGSASNP")

Manual

Documentation can be accessed using:

library(intGSASNP)

ZAEDPolSl/intGSASNP documentation built on Dec. 18, 2021, 8:24 p.m.