Table of Contents
GIFT is a Gene-based Integrative Fine-mapping for performing conditional TWAS analysis. 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 and accounts for the uncertainty in the constructed GReX. As a result, GIFT provides effective type I error control, refines marginal TWAS associations into a much smaller set of putatively causal associations, and yields high statistical power with reduced false discoveries. The software is distributed under the GNU General Public License.
Cite GIFT #
Liu, L., Yan, R., Guo, P. et al. Conditional transcriptome-wide association study for fine-mapping candidate causal genes. Nat Genet 56, 348–356 (2024). https://doi.org/10.1038/s41588-023-01645-y
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if you have questions, feel free to leave messages on the github issues or contact me through email: luliuu@umich.edu
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