README.md

In tangzheng1/PSCAN: Protein-structure-guided scan method for detecting gene-level associations and signal variants

PSCAN v1.1

PSCAN Protein-structure-guided scan methods for gene-level association test and signal region detection

PSCAN package has the main PSCAN function that implements protein-structure-guided scan (PSCAN) methods for detecting gene-level associations and signal variants. PSCAN methods leverage the tendency of functional variants to cluster in 3D protein space. PSCAN methods are built upon flexibly shaped spatial scan statistics, with scan windows adaptively defined to accommodate diverse topologies of variant positions in protein space. PSCAN performs fast gene-level association tests by combining SNP-set-based testing p-values across windows using the Cauchy method. In addition, PSCAN implements an efficient search algorithm for the detection of multiple signal regions in protein space. The method details are described in Tang et al. (2020).

References

Tang ZZ, Sliwoski GR, Chen G, Jin B, Bush WS, Li B, and Capra JA (2020). PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection. Genome Biology.

Installation

PSCAN can be installed from github directly as follows:

install.packages("devtools")
library(devtools)
install_github("tangzheng1/PSCAN")

Tutorial

A vignette with examples illustrating the usage of PSCAN is available at: https://github.com/tangzheng1/PSCAN/blob/master/vignette

Contact

Zheng-Zheng Tang (UW-Madison) [e-mail].

tangzheng1/PSCAN documentation built on Aug. 5, 2020, 2:12 p.m.