This is an R package for performing Q-SCAN procedure in whole genome sequencing studies.
QSCAN is an R package for performing a computationally efficient quadratic scan (Q-SCAN) statistic based method to detect the existence and the locations of signal regions by scanning the genome continuously. The proposed method accounts for the correlation (linkage disequilibrium) among genetic variants, and allows for signal regions to have both causal and neutral variants, and the effects of signal variants to be in different directions.
QSCAN links to R packages Rcpp and RcppArmadillo, and also imports R packages Rcpp, RcppArmadillo and Matrix, These dependencies should be installed before installing QSCAN.
library(devtools)
devtools::install_github("zilinli1988/QSCAN")
Please see the QSCAN user manual for detailed usage of QSCAN package. Please see the QSCAN Example for an example of analyzing sequencing data using Q-SCAN procedure.
If you use QSCAN for your work, please cite:
Zilin Li, Yaowu Liu, and Xihong Lin (2020) "Simultaneous Detection of Signal Regions Using Quadratic Scan Statistics With Applications to Whole Genome Association Studies". JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION. DOI: 10.1080/01621459.2020.1822849.
This software is licensed under GPLv3.