GIFT(Gene-based Integrative Fine-mapping through conditional TWAS), is an R package for efficient statistical inference of conditional TWAS fine-mapping. GIFT examines one genomic region at a time, jointly models the GReX of all genes residing in the focal region, and carries out TWAS conditional analysis in a maximum likelihood framework. In the process, GIFT explicitly models the gene expression correlation and cis-SNP LD across different genes in the region, accounts for the uncertainty in the constructed GReX through joint inference and provides calibrated p values.
It is easy to install the development version of GIFT package using the 'devtools' package.
# install.packages("devtools")
library(devtools)
install_github("yuanzhongshang/GIFT")
The main function in the package is GIFT, you can find the instructions by '?GIFT'.
library(GIFT)
?GIFT
See Tutorial for detailed documentation and examples.
This R package is developed by Lu Liu, Zhongshang Yuan and Xiang Zhou.