The screening and ranking algorithm to detect DNA copy number variations

DOI10.1214/12-AOAS539zbMath1401.92145arXiv1210.0345OpenAlexW2033695946MaRDI QIDQ714382

Heping Zhang, Yue Selena Niu

Publication date: 21 October 2012

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1210.0345

zbMATH Keywords

high dimensional datachange-point detectioncopy number variationsscreening and ranking algorithm

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Statistical ranking and selection procedures (62F07)

Related Items

Multiscale Quantile Segmentation ⋮ Variance change point detection for fractional Brownian motion based on the likelihood ratio test ⋮ Alternating Pruned Dynamic Programming for Multiple Epidemic Change-Point Estimation ⋮ Estimation of change-point models ⋮ Moving Sum Data Segmentation for Stochastic Processes Based on Invariance ⋮ Hypothesis testing for populations of networks ⋮ Data-driven selection of the number of change-points via error rate control ⋮ Multiple change-points detection in high dimension ⋮ Segmentation and estimation of change-point models: false positive control and confidence regions ⋮ A generalized knockoff procedure for FDR control in structural change detection ⋮ Equivariant variance estimation for multiple change-point model ⋮ Outlier reset CUSUM for the exploration of copy number alteration data ⋮ Multiple change point detection and validation in autoregressive time series data ⋮ Covariate assisted screening and estimation ⋮ Multiscale blind source separation ⋮ Two-stage data segmentation permitting multiscale change points, heavy tails and dependence ⋮ The screening and ranking algorithm to detect DNA copy number variations ⋮ Consistent selection of the number of change-points via sample-splitting ⋮ Discussion of “Birnbaum‐Saunders distribution: A review of models, analysis, and applications” ⋮ Authors' Rejoinder ⋮ FDR-control in multiscale change-point segmentation ⋮ Identifying multiple changes for a functional data sequence with application to freeway traffic segmentation ⋮ Bayesian multiple change-points detection in a normal model with heterogeneous variances ⋮ Multiple change-point detection: a selective overview ⋮ Nonparametric maximum likelihood approach to multiple change-point problems ⋮ A shape-based cutting and clustering algorithm for multiple change-point detection ⋮ Sequential model selection-based segmentation to detect DNA copy number variation ⋮ Variance Change Point Detection Under a Smoothly-Changing Mean Trend with Application to Liver Procurement ⋮ A multi-scale approach for testing and detecting peaks in time series

Uses Software

• PennCNV

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Reconstructing DNA copy number by penalized estimation and imputation
• The solution path of the generalized lasso
• The screening and ranking algorithm to detect DNA copy number variations
• Properties and refinements of the fused Lasso
• Estimating the number of change-points via Schwarz' criterion
• On tests for detecting change in mean
• On the estimation of jump points in smooth curves
• Hidden Markov models approach to the analysis of array CGH data
• Pathwise coordinate optimization
• Spatial smoothing and hot spot detection for CGH data using the fused lasso
• Tests for a change-point
• Detection of the number, locations and magnitudes of jumps
• Multiple changepoint fitting via quasilikelihood, with application to DNA sequence segmentation
• Sparsity and Smoothness Via the Fused Lasso
• Circular binary segmentation for the analysis of array-based DNA copy number data
• A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data