Myriads program web page

Departamento de Bioquímica, Genética e Inmunología
Área de Genética. Universidad de Vigo

 

Myriads: p-value-based dependence detection, simulation, and multiple testing correction

The Myriads program presents three main features:

I) Multiple testing correction methods (see below).

 

II) Dependence test: Myriads incorporates an autocorrelation test based on the generalized Durbin-Watson statistic. The test permits to identify strong dependencies in the p-values.

 

III) Simulator: Myriads include the possibility of simulating lists of correlated p-values obtained by conducting

 

i) A two sample t-test for each gene. The size of the effects is user-defined by introducing the desired power for each test.
ii) A Cochran-Armitage trend test for association testing in case-control studies (only from version 1.1).

 

Detailed information on the different features is given in the Supplementary Information document and in the program manual.

 

I) Multiple testing correction methods

 

Sequential Bonferroni (Holm 1979), Benjamini-Hochberg (1995) FDR, SGoF (Carvajal-Rodriguez et al. 2009), SLIM (Wang et al. 2011) and Bon-EV (Li et al. 2017). Myriads also estimates the proportion of true null hypothesis and computes the corresponding q-values (Tibshirani & Storey 2003; Storey et al 2004). The SGoF adjustment can also be computed without a list of p-values via interactive input of the number of comparisons and significant cases detected. The remaining methods need a list of probability values in a text file.

 

Input File

 

The input file is called by default PvalMyriads.dat but any other name can be given from the corresponding option in the menu or argument in the command line. The input file should have an integer number indicating the total number of tests and after it two columns with pairs of identifiers and p-values. The identifier can be a number or a character string.

 

See an Myriads input file example:

 

7

1         0.003
id2     5e-3
gen3      1.0
id4       0.34
5         0.01
6         0.004
7         0.445


There is no limit on the number of p-values other than computer memory. Detailed information about the menu options and the command line arguments can be found in the manual.

 

Run the program

 

a) Windows: double click the Myriads.exe file.
b) Unix/Linux: Just type ./Myriads. The linux executable was compiled in Ubuntu 14.04 . Source will be provided upon request to be compiled in any other system.

 

Output File

 

The program provides with two kinds of output files:

 

1) Myriads.txt which includes only the tests remaining significant after the different adjustments.
2) Myriads_Fulloutput.html and Myriads_Fulloutput.xls which provide with the full list of a priori significant p-values, the adjusted p after each method and the estimated q-values. The .html file returns just the output coming from the last program execution while the .xls accumulate the output through different executions.

 

The adjusted B-H, BonSEV and SB p-values were computed following Yekutieli & Benjamini (1999). When the number of tests is below 10,000 (a myriad), the adjusted p-values for SGoF were computed following (Castro-Conde and de Uña-Álvarez, 2015). For higher number of tests, the SGoF metatest p-values are given by default, the adjusted p-values when computed, follow the approximation developed in (Carvajal-Rodriguez, 2017). Values under the SLIM column correspond to the q-value obtained using the SLIM estimate for the proportion of true nulls.

 

See an Myriads_Fulloutput file example:

 

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