A Generalized Model to Estimate the Statistical Power in Mitochondrial Disease Studies Involving 2×k Tables
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{"title"=>"A Generalized Model to Estimate the Statistical Power in Mitochondrial Disease Studies Involving 2×k Tables", "type"=>"generic", "authors"=>[{"first_name"=>"Jacobo", "last_name"=>"Pardo-Seco", "scopus_author_id"=>"55498820400"}, {"first_name"=>"Jorge", "last_name"=>"Amigo", "scopus_author_id"=>"24464783100"}, {"first_name"=>"Wenceslao", "last_name"=>"González-Manteiga", "scopus_author_id"=>"55396991000"}, {"first_name"=>"Antonio", "last_name"=>"Salas", "scopus_author_id"=>"7102443063"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24086285", "sgr"=>"84884694227", "doi"=>"10.1371/journal.pone.0073567", "scopus"=>"2-s2.0-84884694227", "pui"=>"369903722", "issn"=>"19326203"}, "id"=>"a6a03e2d-157a-3914-b366-226a9db34d0e", "abstract"=>"BACKGROUND: Mitochondrial DNA (mtDNA) variation (i.e. haplogroups) has been analyzed in regards to a number of multifactorial diseases. The statistical power of a case-control study determines the a priori probability to reject the null hypothesis of homogeneity between cases and controls. METHODS/PRINCIPAL FINDINGS: We critically review previous approaches to the estimation of the statistical power based on the restricted scenario where the number of cases equals the number of controls, and propose a methodology that broadens procedures to more general situations. We developed statistical procedures that consider different disease scenarios, variable sample sizes in cases and controls, and variable number of haplogroups and effect sizes. The results indicate that the statistical power of a particular study can improve substantially by increasing the number of controls with respect to cases. In the opposite direction, the power decreases substantially when testing a growing number of haplogroups. We developed mitPower (http://bioinformatics.cesga.es/mitpower/), a web-based interface that implements the new statistical procedures and allows for the computation of the a priori statistical power in variable scenarios of case-control study designs, or e.g. the number of controls needed to reach fixed effect sizes. CONCLUSIONS/SIGNIFICANCE: The present study provides with statistical procedures for the computation of statistical power in common as well as complex case-control study designs involving 2×k tables, with special application (but not exclusive) to mtDNA studies. In order to reach a wide range of researchers, we also provide a friendly web-based tool--mitPower--that can be used in both retrospective and prospective case-control disease studies.", "link"=>"http://www.mendeley.com/research/generalized-model-estimate-statistical-power-mitochondrial-disease-studies-involving-2k-tables", "reader_count"=>10, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>1, "Other"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>1, "Other"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>5, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Spain"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1218387", "https://ndownloader.figshare.com/files/1218389"], "description"=>"<div><p>Background</p><p>Mitochondrial DNA (mtDNA) variation (i.e. haplogroups) has been analyzed in regards to a number of multifactorial diseases. The statistical power of a case-control study determines the <i>a priori</i> probability to reject the null hypothesis of homogeneity between cases and controls.</p><p>Methods/Principal Findings</p><p>We critically review previous approaches to the estimation of the statistical power based on the restricted scenario where the number of cases equals the number of controls, and propose a methodology that broadens procedures to more general situations. We developed statistical procedures that consider different disease scenarios, variable sample sizes in cases and controls, and variable number of haplogroups and effect sizes. The results indicate that the statistical power of a particular study can improve substantially by increasing the number of controls with respect to cases. In the opposite direction, the power decreases substantially when testing a growing number of haplogroups. We developed mitPower (<a href=\"http://bioinformatics.cesga.es/mitpower/\" target=\"_blank\">http://bioinformatics.cesga.es/mitpower/</a>), a web-based interface that implements the new statistical procedures and allows for the computation of the <i>a priori</i> statistical power in variable scenarios of case-control study designs, or e.g. the number of controls needed to reach fixed effect sizes.</p><p>Conclusions/Significance</p><p>The present study provides with statistical procedures for the computation of statistical power in common as well as complex case-control study designs involving 2×<i>k</i> tables, with special application (but not exclusive) to mtDNA studies. In order to reach a wide range of researchers, we also provide a friendly web-based tool – mitPower – that can be used in both retrospective and prospective case-control disease studies.</p></div>", "links"=>[], "tags"=>["generalized", "mitochondrial", "studies", "involving", "tables"], "article_id"=>810042, "categories"=>["Uncategorised"], "users"=>["Jacobo Pardo-Seco", "Jorge Amigo", "Wenceslao González-Manteiga", "Antonio Salas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0073567.s001", "https://dx.doi.org/10.1371/journal.pone.0073567.s002"], "stats"=>{"downloads"=>9, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Generalized_Model_to_Estimate_the_Statistical_Power_in_Mitochondrial_Disease_Studies_Involving_2_k_Tables/810042", "title"=>"A Generalized Model to Estimate the Statistical Power in Mitochondrial Disease Studies Involving 2×<i>k</i> Tables", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-09-27 02:00:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/1218382"], "description"=>"<p>The right side shows power corrected according to <i>N<sub>H</sub></i>, and the nonparametric estimated regression curve. Colored circles denote different number of haplogroups; black: 4 haplogroups; red: 8 haplogroups; green: 12 haplogroups; dark blue: 16; and light blue: 20. Haplogroup frequencies were built using a vector of probabilities where the risk allele takes values 0.30, 0.15 or 0.05 (other values led to the same results; data not shown). The risky haplogroup take relative frequency differences in cases with respect to control of 100%, 50% and 25%. The number of cases takes values of 100, 250, 500, 750 and 1000, and control-case odds of 1, 2 and 3. We noted that other values do not change the distribution. The red line indicates the theoretical curve for 2×2 tables and equal numbers of cases and controls, while the black line is the non-parametric estimator of regression between <i>N<sub>sc</sub></i> parameter and the statistical power.</p>", "links"=>[], "tags"=>["shows", "correction", "haplogroups", "cases", "equals"], "article_id"=>810037, "categories"=>["Uncategorised"], "users"=>["Jacobo Pardo-Seco", "Jorge Amigo", "Wenceslao González-Manteiga", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073567.g003", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_left_side_shows_power_values__0_05_as_a_function_of_N_sc_without_correction_of_number_of_haplogroups_N_H_for_different_number_of_haplogroups_and_when_the_number_of_cases_equals_the_number_of_controls_/810037", "title"=>"The left side shows power values (α = 0.05) as a function of <i>N<sub>sc</sub></i> without correction of number of haplogroups (<i>N<sub>H</sub></i>) for different number of haplogroups and when the number of cases equals the number of controls.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-27 02:00:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/1218381"], "description"=>"<p>The intensity of the symbols indicate different odds ratio control-case: the thinner symbols indicate odds 1∶1, the medium symbols odds 2∶1, while the bolded symbols odds 3∶1. Colors indicate different deviations from the null hypothesis; black: the frequency of the risky allele is 100% higher in cases than in controls, red: 50%; and green 25%. The graph indicates that there is not a relationship between the number of cases and the statistical power value. On the right side are the power values as a function of the statistic <i>N<sub>sc</sub></i>; in red is the theoretical curve for the statistical power for 2×2 tables when the number of controls is equal to the number of cases.</p>", "links"=>[], "tags"=>["cases", "haplogroups", "circles", "haplogroup", "triangles", "crosses"], "article_id"=>810036, "categories"=>["Uncategorised"], "users"=>["Jacobo Pardo-Seco", "Jorge Amigo", "Wenceslao González-Manteiga", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073567.g002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_On_the_left_side_are_the_power_values_945_8202_8202_0_05_as_a_function_of_the_number_of_cases_for_different_haplogroups_the_circles_refer_to_haplogroup_H_triangles_to_haplogroup_J_and_crosses_to_haplogroup_I_/810036", "title"=>"On the left side are the power values (α = 0.05) as a function of the number of cases for different haplogroups (the circles refer to haplogroup H, triangles to haplogroup J and crosses to haplogroup I).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-27 02:00:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/1218384"], "description"=>"<p>These values were averaged over ten simulations each. Note that these values differ slightly from those obtained by Samuels et al. (see their Table 3) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073567#pone.0073567-Samuels1\" target=\"_blank\">[26]</a> due to the simulation procedure implemented in both studies and because we consider unequal number of cases and controls.</p>", "links"=>[], "tags"=>["estimates", "non-parametric"], "article_id"=>810039, "categories"=>["Uncategorised"], "users"=>["Jacobo Pardo-Seco", "Jorge Amigo", "Wenceslao González-Manteiga", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073567.t002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_estimates_for_a_significance_level_and_a_power_value_using_non_parametric_regression_/810039", "title"=>"estimates for a significance level α and a power value β using non-parametric regression.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-27 02:00:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/1218385"], "description"=>"<p>Estimates were computed for 1,000 and 10,000 simulated tables (ST), number of cases equal to number of controls, and level of significance α = 0.05 (therefore, estimated power values should be close to 5%). Time estimates were obtained using an Intel® Core™ I5 3.1 GHz. These values were averaged over ten simulations each.</p>", "links"=>[], "tags"=>["null", "asymptotic", "permutation", "elapsed", "computational", "times", "simulation"], "article_id"=>810040, "categories"=>["Uncategorised"], "users"=>["Jacobo Pardo-Seco", "Jorge Amigo", "Wenceslao González-Manteiga", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073567.t001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_statistical_power_under_the_null_hypothesis_using_the_asymptotic_distribution_versus_the_permutation_procedure_and_elapsed_computational_times_in_seconds_under_different_simulation_scenarios_/810040", "title"=>"Estimates of statistical power (%) under the null hypothesis using the asymptotic distribution <i>versus</i> the permutation procedure, and elapsed computational times (in seconds) under different simulation scenarios.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-27 02:00:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/1218383"], "description"=>"<p>See legend of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073567#pone-0073567-g003\" target=\"_blank\"><b>Figure 3</b></a> for more information on the simulation.</p>", "links"=>[], "tags"=>["simulations", "parameter", "raised", "empirically", "allows", "scenarios", "cases", "differs"], "article_id"=>810038, "categories"=>["Uncategorised"], "users"=>["Jacobo Pardo-Seco", "Jorge Amigo", "Wenceslao González-Manteiga", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073567.g004", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_simulations_show_that_the_parameter_N_H_raised_to_the_power_of_0_37_is_the_one_that_empirically_allows_a_better_fit_of_the_data_to_the_theoretical_curve_of_statistical_power_even_in_scenarios_where_the_number_of_cases_differs_from_the_number_of_contr/810038", "title"=>"The simulations show that the parameter <i>N<sub>H</sub></i> raised to the power of 0.37 is the one that empirically allows a better fit of the data to the theoretical curve of statistical power even in scenarios where the number of cases differs from the number of controls.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-27 02:00:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/1218380"], "description"=>"<p>Colors indicate different deviations from the null hypothesis; thus, black represents a frequency in cases 100% higher than in controls, red represents an increment of 50%, and green an increment of 25% (with the difference distributed proportionally between the remaining non-risky haplogroups). The different lines indicate different case-control odds. The continuous line denotes an odd control-case of 1∶1, the dotted line of 2∶1, and the pointed line of 3∶1. Frequencies in controls for each haplogroup are indicated above each plot. Note that the results can be directly comparable with Samuels et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073567#pone.0073567-Samuels1\" target=\"_blank\">[26]</a> (see their <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073567#pone-0073567-g001\" target=\"_blank\"><b>Figure</b> 1</a>) when number of cases equals number of controls.</p>", "links"=>[], "tags"=>["haplogroups", "cases", "chi-square"], "article_id"=>810035, "categories"=>["Uncategorised"], "users"=>["Jacobo Pardo-Seco", "Jorge Amigo", "Wenceslao González-Manteiga", "Antonio Salas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0073567.g001", "stats"=>{"downloads"=>2, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representation_of_power_values_for_three_haplogroups_H_J_and_I_as_a_function_of_the_number_of_cases_and_using_the_Chi_square_test_significance_level_945_8202_8202_0_05_/810035", "title"=>"Representation of power values for three haplogroups (H, J. and I) as a function of the number of cases and using the Chi-square test (significance level α = 0.05).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-27 02:00:31"}

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  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Biology and life sciences/Population biology", "average_usage"=>[269, 448, 558, 658, 744, 830, 914, 995, 1068, 1139, 1214, 1284, 1349]}, {"subject_area"=>"/Computer and information sciences", "average_usage"=>[297, 488, 616, 724, 828, 939, 1038, 1127, 1223, 1311, 1393, 1479, 1556]}, {"subject_area"=>"/Physical sciences/Mathematics", "average_usage"=>[259, 431, 541, 639, 727, 816, 898, 980, 1061, 1136, 1214, 1294, 1356]}]}
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