TY - GEN
T1 - Identification of significant genetic variants via SLOPE, and its extension to Group SLOPE
AU - Gossmann, Alexej
AU - Cao, Shaolong
AU - Wang, Yu Ping
N1 - Publisher Copyright:
Copyright 2015 ACM.
PY - 2015/9/9
Y1 - 2015/9/9
N2 - The method of Sorted L-One Penalized Estimation, abbreviated as SLOPE, is a novel sparse regression method for model selection introduced in a sequence of recent papers, [4], [3] and [7] by Bogdan, van den Berg, Sabatti, Su and Candes. It estimates the coefficients of a linear model that possibly has more unknown parameters than observations. In many settings the SLOPE method is shown to successfully control the false discovery rate (the proportion of the irrelevant among all selected predictors) at a user specified level. In this paper we evaluate its performance on genetic data, and show its superiority over LASSO which is a related and popular method. Often in genetic data sets, group structures among the predictor variables are given as prior knowledge, such as SNPs in a gene or genes in a pathway. Following this motivation we extend SLOPE in the spirit of Group LASSO to Group SLOPE, a method that can handle group structures between the predictor variables, which are ubiquitous in real genetic data. Our simulation results show that the proposed Group SLOPE method is capable of controlling the false discovery rate at a specified level. Moreover, our simulations show that compared to Group LASSO, Group SLOPE in general achieves a higher power as well as a lower false discovery rate.
AB - The method of Sorted L-One Penalized Estimation, abbreviated as SLOPE, is a novel sparse regression method for model selection introduced in a sequence of recent papers, [4], [3] and [7] by Bogdan, van den Berg, Sabatti, Su and Candes. It estimates the coefficients of a linear model that possibly has more unknown parameters than observations. In many settings the SLOPE method is shown to successfully control the false discovery rate (the proportion of the irrelevant among all selected predictors) at a user specified level. In this paper we evaluate its performance on genetic data, and show its superiority over LASSO which is a related and popular method. Often in genetic data sets, group structures among the predictor variables are given as prior knowledge, such as SNPs in a gene or genes in a pathway. Following this motivation we extend SLOPE in the spirit of Group LASSO to Group SLOPE, a method that can handle group structures between the predictor variables, which are ubiquitous in real genetic data. Our simulation results show that the proposed Group SLOPE method is capable of controlling the false discovery rate at a specified level. Moreover, our simulations show that compared to Group LASSO, Group SLOPE in general achieves a higher power as well as a lower false discovery rate.
KW - False discovery rate
KW - Group LASSO
KW - LASSO
KW - SLOPE
KW - Sparse regression
UR - http://www.scopus.com/inward/record.url?scp=84963616437&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84963616437&partnerID=8YFLogxK
U2 - 10.1145/2808719.2808743
DO - 10.1145/2808719.2808743
M3 - Conference contribution
AN - SCOPUS:84963616437
T3 - BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
SP - 232
EP - 240
BT - BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
PB - Association for Computing Machinery, Inc
T2 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2015
Y2 - 9 September 2015 through 12 September 2015
ER -