Simpute: An Efficient Solution for Dense Genotypic Data
Joint Authors
Hsieh, Wen-Ping
Chang, Chun-Tien
Lin, Yen-Jen
Tang, Chuan Yi
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-7, 7 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-02-03
Country of Publication
Egypt
No. of Pages
7
Main Subjects
Abstract EN
Single nucleotide polymorphism (SNP) data derived from array-based technology or massive parallel sequencing are often flawed with missing data.
Missing SNPs can bias the results of association analyses.
To maximize information usage, imputation is often adopted to compensate for the missing data by filling in the most probable values.
To better understand the available tools for this purpose, we compare the imputation performances among BEAGLE, IMPUTE, BIMBAM, SNPMStat, MACH, and PLINK with data generated by randomly masking the genotype data from the International HapMap Phase III project.
In addition, we propose a new algorithm called simple imputation (Simpute) that benefits from the high resolution of the SNPs in the array platform.
Simpute does not require any reference data.
The best feature of Simpute is its computational efficiency with complexity of order (mw+n), where n is the number of missing SNPs, w is the number of the positions of the missing SNPs, and m is the number of people considered.
Simpute is suitable for regular screening of the large-scale SNP genotyping particularly when the sample size is large, and efficiency is a major concern in the analysis.
American Psychological Association (APA)
Lin, Yen-Jen& Chang, Chun-Tien& Tang, Chuan Yi& Hsieh, Wen-Ping. 2013. Simpute: An Efficient Solution for Dense Genotypic Data. BioMed Research International،Vol. 2013, no. 2013, pp.1-7.
https://search.emarefa.net/detail/BIM-1005182
Modern Language Association (MLA)
Lin, Yen-Jen…[et al.]. Simpute: An Efficient Solution for Dense Genotypic Data. BioMed Research International No. 2013 (2013), pp.1-7.
https://search.emarefa.net/detail/BIM-1005182
American Medical Association (AMA)
Lin, Yen-Jen& Chang, Chun-Tien& Tang, Chuan Yi& Hsieh, Wen-Ping. Simpute: An Efficient Solution for Dense Genotypic Data. BioMed Research International. 2013. Vol. 2013, no. 2013, pp.1-7.
https://search.emarefa.net/detail/BIM-1005182
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1005182