Description Usage Arguments Details Value

FDR threshold and SNP highlighting

1 | ```
fdr_thresh(gwas_results, id, p, meth = "fdr", thresh = 0.05)
``` |

`gwas_results` |
A dataframe containing at least the following columns: 1) SNP identifiers 2) GWAS p-values. These should NOT be -log transformed |

`id` |
String specifying the name of the column in gwas_results containing SNP identifiers |

`p` |
Character specifying the name of the column in gwas_results containing GWAS output p-values |

`meth` |
String specifying the method of p-value adjustment to use - see output of help(p.adjust) for details |

`thresh` |
Number between 0 and 1 - the desired FDR threshold |

Adjusted p-values are calculated from a vector of p-values output from a GWAS analysis. If any adjusted p-values fall below the specified threshold, an approximate threshold for adjusted p-values is returned, with a list of the IDs of significant SNPs

list consisting of

`p.thresh` |
approximation of the FDR threshold for p-value distribution |

`sig.snps` |
vector of names of SNPs passing the FDR threshold |

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