haplo.stats statistics

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haplo.stats specifications


Unique identifier OMICS_10169
Name haplo.stats
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.7.9
Stability Stable
methods, stats, graphics, R.rsp, R(≥3.0.0), rms
Maintained Yes


No version available



  • person_outline Jason Sinnwell

Publications for haplo.stats

haplo.stats citations


Genome wide haplotype association analysis of primary biliary cholangitis risk in Japanese

Sci Rep
PMCID: 5958065
PMID: 29773854
DOI: 10.1038/s41598-018-26112-1

[…] We used the R “haplo.stats” package, commonly employed in secondary explorations of haplotypes in single-SNP GWAS,, as our benchmark haplotype association analysis method. This method is used to obtain maximum likel […]


HLA class II haplotypes and Autism Spectrum Disorders

Sci Rep
PMCID: 5955937
PMID: 29769579
DOI: 10.1038/s41598-018-25974-9

[…] edictive variables. By default, calculations assume that a two-tailed statistical test was used at a confidence level of 95%.All analyses were performed with R version 3.2.0 (2015-04-16). The package haplo.stats (version 1.7.1) was used for the haplotype study. […]


Genetic Polymorphism at CCL5 Is Associated With Protection in Chagas’ Heart Disease: Antagonistic Participation of CCR1+ and CCR5+ Cells in Chronic Chagasic Cardiomyopathy

Front Immunol
PMCID: 5904358
PMID: 29696014
DOI: 10.3389/fimmu.2018.00615

[…] Genetic analyses were performed in R environment version 3.3.3 with the following packages: coin, epiDisplay, gap, genetics, haplo.stats, and SNPassoc. Comparisons among demographic or clinical variables were performed either by the chi-square test or Kruskal–Wallis test when appropriate. The association of genotypic and mi […]


Association of circadian rhythm genes ARNTL/BMAL1 and CLOCK with multiple sclerosis

PLoS One
PMCID: 5764259
PMID: 29324865
DOI: 10.1371/journal.pone.0190601

[…] nce values for multiple testing were applied using the Benjamini-Hochberg correction method (false-discovery rate–FDR values) as multiple SNPs were analysed.Haplotype frequencies were estimated using haplo.stats package 16 []. The haplo.score function was used to directly ascertain differences in haplotype distributions across the groups of MS patients and healthy controls. A global test of associ […]


Association between glutamate transporter gene polymorphisms and obsessive compulsive disorder/trait empathy in a South Korean population

PLoS One
PMCID: 5755803
PMID: 29304071
DOI: 10.1371/journal.pone.0190593
call_split See protocol

[…] ium (LD)’ approach in the control sample using Haploview v4.0 []. Associations between haplotype distributions and OCD under additive model were examined using the ‘haplo.score’ function of R package haplo.stats [], while adjusting for age and sex.In order to analyze the relationship between SLC1A1 variants and certain aspects of empathy measured with IRI, we used all available IRI data that were […]


Genetic Variants of the Receptor for Advanced Glycation End products in Susceptibility to Type 2 Diabetes Mellitus in Primary Hypertensive Patients

Sci Rep
PMCID: 5722821
PMID: 29222432
DOI: 10.1038/s41598-017-17068-9
call_split See protocol

[…] association magnitude between the RAGE gene and T2DM risk in primary hypertensive patients. Moreover, the frequencies of haplotypes based on 4 significant variants were estimated by using the program Haplo.Stats, version 1.7.7 developed by Sinnwell and Schaid (http://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software). The omnibus association of derived haplotypes as a w […]


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haplo.stats institution(s)
Mayo Clinic/Foundation, Chinahester, MN, USA

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