gwid: an R package and Shiny application for Genome-Wide analysis of IBD data

被引：1

作者：

Mahmoudiandehkordi, Soroush ^{[1
,2
]}

Maadooliat, Mehdi ^{[1
,2
]}

Schrodi, Steven J. ^{[2
,3
]}

机构：

[1] Marquette Univ, Dept Math & Stat Sci, Milwaukee, WI 53233 USA

[2] Univ Wisconsin Madison, Dept Med Genet, 425-g Henry Mall, Madison, WI 53706 USA

[3] Univ Wisconsin Madison, Computat & Informat Biol & Med, Madison, WI 53706 USA

来源：

BIOINFORMATICS ADVANCES | 2024年 / 4卷 / 01期

关键词：

IDENTITY; DESCENT; ASSOCIATION;

D O I：

10.1093/bioadv/vbae115

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Genome-wide identity by descent (gwid) is an R package developed for the analysis of identity-by-descent (IBD) data pertaining to dichotomous traits. This package offers a set of tools to assess differential IBD levels for the two states of a binary trait, yielding informative and meaningful results. Furthermore, it provides convenient functions to visualize the outcomes of these analyses, enhancing the interpretability and accessibility of the results. To assess the performance of the package, we conducted an evaluation using real genotype data derived from the SNPs to investigate rheumatoid arthritis susceptibility from the Marshfield Clinic Personalized Medicine Research Project.

引用

页数：5

共 20 条

[1] A tutorial on statistical methods for population association studies [J].

Balding, David J. .

NATURE REVIEWS GENETICS, 2006, 7 (10) :781-791

[2] Genome-wide association studies using a penalized moving-window regression [J].

Bao, Minli ;

Wang, Kai .

BIOINFORMATICS, 2017, 33 (24) :3887-3894

[3] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].

BENJAMINI, Y ;

HOCHBERG, Y .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300

[4] Fast two-stage phasing of large-scale sequence data [J].

Browning, Brian L. ;

Tian, Xiaowen ;

Zhou, Ying ;

Browning, Sharon R. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2021, 108 (10) :1880-1890

[5] A One-Penny Imputed Genome from Next-Generation Reference Panels [J].

Browning, Brian L. ;

Zhou, Ying ;

Browning, Sharon R. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2018, 103 (03) :338-348

[6] Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data [J].

Browning, Brian L. ;

Browning, Sharon R. .

GENETICS, 2013, 194 (02) :459-+

[7] Identity by Descent Between Distant Relatives: Detection and Applications [J].

Browning, Sharon R. ;

Browning, Brian L. .

ANNUAL REVIEW OF GENETICS, VOL 46, 2012, 46 :617-633

[8] Detecting Rare Variant Associations by Identity-by-Descent Mapping in Case-Control Studies [J].

Browning, Sharon R. ;

Thompson, Elizabeth A. .

GENETICS, 2012, 190 (04) :1521-1531

[9] The role of haplotypes in candidate gene studies [J].

Clark, AG .

GENETIC EPIDEMIOLOGY, 2004, 27 (04) :321-333

[10] Next-generation genotype imputation service and methods [J].

Das, Sayantan ;

Forer, Lukas ;

Schoenherr, Sebastian ;

Sidore, Carlo ;

Locke, Adam E. ;

Kwong, Alan ;

Vrieze, Scott I. ;

Chew, Emily Y. ;

Levy, Shawn ;

McGue, Matt ;

Schlessinger, David ;

Stambolian, Dwight ;

Loh, Po-Ru ;

Iacono, William G. ;

Swaroop, Anand ;

Scott, Laura J. ;

Cucca, Francesco ;

Kronenberg, Florian ;

Boehnke, Michael ;

Abecasis, Goncalo R. ;

Fuchsberger, Christian .

NATURE GENETICS, 2016, 48 (10) :1284-1287

← 1 2 →