SNPassoc protocols

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SNPassoc specifications

Information


Unique identifier OMICS_10116
Name SNPassoc
Software type Package/Module
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 1.9-2
Stability Stable
Requirements
parallel, survival, mvtnorm, R(≥3.0.0), haplo.stats
Maintained Yes

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Maintainer


  • person_outline Juan R. González <>

Publication for SNPassoc

SNPassoc in pipelines

 (6)
2018
PMCID: 5755803
PMID: 29304071
DOI: 10.1371/journal.pone.0190593

[…] regression analyses. the genetic model was assumed as additive (i.e., genotypes were coded as 0, 1, and 2 based on the minor allele count). single-marker analyses were performed using the r package snpassoc []. in haplotype analyses, haplotype blocks of the six slc1a1 snps were defined based on the ‘solid spine of linkage disequilibrium (ld)’ approach in the control sample using haploview v4.0 […]

2016
PMCID: 4891883
PMID: 27255376
DOI: 10.1186/s12936-016-1350-2

[…] with one-way analysis of variance (anova). correlation coefficients of the antibody levels were estimated with the pearson correlation. interactions between snp pairs were also assessed with the ‘snpassoc’ package, which determines the effects of interaction by means of log-likelihood ratio tests (lrts)., haplotype blocks were determined with haploview 4.2 using the solid spine of linkage […]

2016
PMCID: 5018838
PMID: 27616601
DOI: 10.1038/srep32564

[…] with the genotype as an independent variable and the ds-r subscales as dependent variables. analyses were conducted using the r software (version 3.2.1; http://www.r-project.org) and the r package snpassoc. the overall statistical significance was set at α = 0.005 after bonferroni correction for the 10 independent snps examined. an association was regarded as significant for p < 0.005 […]

2015
PMCID: 4480968
PMID: 26107257
DOI: 10.1371/journal.pone.0130790

[…] groups, we used student t-test. mann-whitney u test was used to analyze non-parametric variables. all tests were done using graphpad instat software (graphpad instat software, san diego, ca) and snpassoc version 1.8‐1 software (catalan institute of oncoloy, barcelona, spain). the odds ratio and 95% confidential intervals were also calculated using the same software. linkage disequilibrium […]

2013
PMCID: 3706890
PMID: 23311897
DOI: 10.1186/gm405

[…] slco2b1 gene was performed with haploview [] using results from our study population of 143 caucasians. haplotype analysis was performed with r-package haplo.stats-1.4.4 [] (r-2.13.0)., r-package snpassoc-1.6-0 was applied to study associations between each variant and oatp expression, with correction for non-genetic (table ) and transcription factors (hnf1α, sp1, ahr, lxrα, fxr, car, hnf3β). […]


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SNPassoc in publications

 (104)
PMCID: 5937760
PMID: 29734345
DOI: 10.1371/journal.pone.0196793

[…] the hapmap collections [], were used for quality control (table b in ). two snps (rs10520789 and rs1679568) did not follow the hardy–weinberg equilibrium and were excluded. the r statistical package snpassoc was used for hardy-weinberg equilibrium assessment and allelic frequency calculation []., the main outcome of treatment was δdas28 at 6 months. eular non-responders compared with responders […]

PMCID: 5940118
PMID: 29676995
DOI: 10.18632/aging.101420

[…] intervals (95% ci) were estimated by using cox proportional hazard models taking also into account possible confounder variables (age and gender)., statistical analyses have been performed using snpassoc and surv packages of r (http://www.r-project.org/)., the functionality of theassociated snps was explored by retrieving regulatory information from the encode […]

PMCID: 5898725
PMID: 29652911
DOI: 10.1371/journal.pone.0194842

[…] plot (mds) and three dimensional mds (3d mds) from the same data., the genotype frequencies of the selected vip in tunisian population, were calculated and compared with 10 hapmap populations, using snpassoc r package []. in this step of analysis, we have considered only the hapmap project populations due to the complete genotypic data. the inter-ethnic genotypic frequency comparison […]

PMCID: 5900548
PMID: 29686695
DOI: 10.3389/fgene.2018.00112

[…] with lipid level variations. genetic modeling of the significant variants was also performed. all these tests were performed using the r software (version 3.3.1) utilizing the following packages snpassoc, psych, genetics, and mass (r core team, ). person's chi-square test was also used to investigate the significant of the different distribution of haplotypes frequencies between the high […]

PMCID: 5902459
PMID: 29692678
DOI: 10.1002/rmb2.12093

[…] study to examine the association of the haplotypes of each gene with the subsequent miscarriage by using age as a covariate. these statistical analyses were conducted using r software, including the snpassoc and haplo.stat packages., furthermore, the differences in the expression levels of the pd1 and pdl1 genes were analyzed in the endometrium of the luteal phase between the patients with rpl […]


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SNPassoc institution(s)
Unit of Biostatistics and Bioinformatics, Epidemiology Service, IDIBELL, Catalan Institute of Oncology, Barcelona, Spain

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