| DiscreteQvalue-package {DiscreteQvalue} | R Documentation |
Improved q-values for discrete uniform and homogeneous tests
Description
This package implements five different versions of the q-value multiple testing procedure
proposed by Storey and Tibshirani (2003). The q-value method
is based on the false discovery rate (FDR); different versions of the q-value method can be defined depending
on the particular estimator used for the proportion of true null hypotheses, \pi_0, which is plugged in the FDR formula. The
first version of the q-value uses the \pi_0 estimator in Storey (2002), with tunning parameter \lambda = 0.5; whereas
the second version uses the \pi_0 estimator in Storey and Tibshirani (2003), which is based on an automatic method to
select the tunning parameter
\lambda. These two methods are only appropriate when the P-values follow a continuous uniform distribution
under the global null hypothesis. This package also provides three other versions of the q-value for
homogeneous discrete uniform P-values, which often appear in practice.
The first discrete version of the q-value uses the \pi_0 estimator
proposed in Liang (2016).
The second discrete q-value method uses the estimator of \pi_0 proposed in Chen et al. (2014),
when simplified for the special case of homogeneous discrete P-values.
The third discrete version of the q-value employs a standard procedure but applied on randomized P-values.
Once the estimated q-values are computed, the q-value method
rejects the null hypotheses whose q-values are less than or equal to the nominal FDR level. All the versions of
the q-value method explained above can be seen in Cousido-Rocha et al. (2019).
Details
Package: ‘DiscreteQvalue’
Version: 1.0
Maintainer: Marta Cousido Rocha martacousido@uvigo.es
License: GPL-2
Value
‘DQ’
Acknowledgements
This work has received financial support of the Call 2015 Grants for PhD contracts for training of doctors of the Ministry of Economy and Competitiveness, co-financed by the European Social Fund (Ref. BES-2015-074958). The authors acknowledge support from MTM2014-55966-P project, Ministry of Economy and Competitiveness, and MTM2017-89422-P project, Ministry of Economy, Industry and Competitiveness, State Research Agency, and Regional Development Fund, UE. The authors also acknowledge the financial support provided by the SiDOR research group through the grant Competitive Reference Group, 2016-2019 (ED431C 2016/040), funded by the “Consellería de Cultura, Educación e Ordenación Universitaria. Xunta de Galicia”.
Author(s)
Marta Cousido Rocha.
José Carlos Soage González.
Jacobo de Uña Álvarez.
Sebastian Döhler.
References
Chen, X., R. W. Doerge, and J. F. Heyse (2014). Methodology Multiple testing with discrete data: proportion of true null hypotheses and two adaptive FDR procedures. arXiv:1410.4274v2.
Cousido-Rocha, M., J. de Uña-Álvarez, and S. Döhler (2019). Multiple testing methods for homogeneous discrete uniform P-values. Preprint.
Liang, K. (2016). False discovery rate estimation for large-scale homogeneous discrete p-values. Biometrics 72, 639-648.
Storey, J. D. (2002). A direct approach to false discovery rates. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 64 (3), 479-498.
Storey, J. and R. Tibshirani (2003). Statistical significance for genomewide studies. Proceedings of National Academy of Science 100, 9440-9445.