Description Usage Arguments Details Value Author(s) References Examples

Based on a given vector of chi-square test statistics, provides estimates of local false discoveries.

1 | ```
LFDR.MM(x)
``` |

`x` |
A vector of chi-square test statistics with one degree of freedom. |

For *N* given features (genes, proteins, SNPs, etc.), the function tests the null hypothesis *H_{0i}*, *i=1,…,N*, indicating that there is no association between feature *i* and a specific disease, versus its alternative hypothesis *H_{1i}*. For each unassociated feature *i*, it is suppoed that the corresponding test stiatistic *x_i* follows a central chi-square distribution with one degree of freedom. For each associated feature *i*, it is assumed that the corresponding test stiatistic *x_i* follows a non-central chi-square distribution with one degree of freedom and non-centrality parameter *λ*. In this packag, association is measured by estimating the local false discovery rate (LFDR), the posterior probability that the null hypothesis *H_{0i}* given the test statistic *x_i* is true.
This package returns three components as mentioned in the **Value** section.

Outputs three elements as seen below:

`pi0.hat` |
estimate of proportion of unassocaited features |

`ncp.hat` |
estimate of the non-centrality parameter |

`lfdr.hat` |
estimates of local false discovery rates. |

Code: Ali Karimnezhad.

Documentation: Ali Karimnezhad.

Karimnezhad, A. (2020). A Simple Yet Efficient Parametric Method of Local False Discovery Rate Estimation Designed for Genome-Wide Association Data Analysis. Retrieved from https://arxiv.org/abs/1909.13307

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
# vector of test statistics for assocaited features
stat.assoc<- rchisq(n=1000,df=1, ncp = 3)
# vector of test statistics for unassocaited features
stat.unassoc<- rchisq(n=9000,df=1, ncp = 0)
# vector of test statistics
stat<- c(stat.assoc,stat.unassoc)
output <- LFDR.MM(x=stat)
# Estimated pi0
output$p0.hat
# Estimated non-centrality parameter
output$ncp.hat
# Estimated LFDRs
output$lfdr.hat
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.