haplo.stats protocols

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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


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  • person_outline Jason Sinnwell <>

Publications for haplo.stats

haplo.stats in pipelines

PMCID: 5755803
PMID: 29304071
DOI: 10.1371/journal.pone.0190593

[…] (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 […]

PMCID: 4891883
PMID: 27255376
DOI: 10.1186/s12936-016-1350-2

[…] blocks were determined with haploview 4.2 using the solid spine of linkage disequilibrium (ld) method [], and the degree of ld between snps was estimated with the d’ parameter. the r package ‘haplo.stats’ [] was used for association tests between haplotypes and antibody levels by means of the ‘haplo.glm’ function, which performs a regression that estimates the effect of each haplotype […]

PMCID: 5018838
PMID: 27616601
DOI: 10.1038/srep32564

[…] pairwise ld patterns of the examined snps. haplotype blocks were defined by the solid spine of ld method with a d′ threshold of 0.8. haplotype-based associations were analysed using the r package haplo.stats, which estimates haplotype frequencies with an expectation-maximization algorithm. haplotype-specific score statistics were computed to test for associations between the haplotype […]

PMCID: 4277309
PMID: 25541704
DOI: 10.1371/journal.pone.0115770

[…] procr genomic region . the ld calculation was based on the control individuals and included procr variants with maf ≥1%., full-length haplotype analyses were done for the case-control group with the haplo stats package v1.4.4 in r (version 3.1.0; http://www.r-project.org), including reconstructed haplotypes with estimated global frequencies ≥1%. in addition, sub-haplotypes were evaluated […]

PMCID: 3672107
PMID: 23750206
DOI: 10.1371/journal.pone.0064164

[…] all 69 snps from cohort 1 series. the snp haplotypes for this cohort were submitted to association analyses with load risk using an additive model, and controlling for the covariates above, within haplo.stats . multilocus genotype analyses (mlgs) were done as previously described . mlgs are defined by the combination of minor allele counts at all of the snp loci, where each locus has 0, 1 or 2 […]

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haplo.stats in publications

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

[…] of selected haplotypes). we further required odds ratios in the replication cohort to have the same direction as the discovery cohort to consider a 3-snp haplotype as replicated., 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 […]

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

[…] 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., marion leboyer and ryad tamouza jointly supervised this work., publisher's note: springer nature remains neutral with regard […]

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

[…] 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 […]

PMCID: 5722821
PMID: 29222432
DOI: 10.1038/s41598-017-17068-9

[…] 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 […]

PMCID: 5712579
PMID: 29238301
DOI: 10.3389/fphar.2017.00879

[…] chi-square test and fisher’s exact test were used to describe the differences in frequencies of the hla-a, b alleles between the groups. haplotype association analysis was carried out using the “haplo.stats” package. the level of statistical significance was set at p < 0.05 (two-sided)., dna samples from 15 ltg-induced cadr patients (10 cases with mpe, 4 cases with sjs, and 1 case […]

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

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