flashfm.input | R Documentation |

Key input for flashfm - constructs snpmod object list and joint effect estimates list for all trait if have external single trait fine-mapping results

flashfm.input( modPP.list, beta1.list, Gmat, Nall, ybar.all, related = FALSE, y = NULL, Nsame = NULL, is.snpmat, raf = NULL )

`modPP.list` |
list of data.frame objects for each trait, containing a column named "snps": snp models of the form |

`beta1.list` |
list of single SNP effect estimates for each trait in the form of a named vector; name of each effect estimate should appear in Gmat |

`Gmat` |
genotype matrix with SNP columns; could be from sample or reference panel; use unrelated samples |

`Nall` |
vector of sample sizes; if related samples then give effective sample sizes |

`ybar.all` |
vector of trait means; if related samples, this should be based on unrelated samples; if traits are transformed to be standard Normal, could set ybar as 0-vector |

`related` |
logical indicating if samples are related (TRUE) or not (FALSE); default is FALSE |

`y` |
(optional) matrix of trait values (trait columns) or indicators of trait measured; used to get joint sample counts; default is NULL and if not provided an approximation is used based on vector of trait sample sizes |

`Nsame` |
(optional) single sample size value, if all traits measured on all individuals |

`is.snpmat` |
logical taking value TRUE when Gmat is a genotype matrix and FALSE when Gmat is a SNP covariance matrix |

`raf` |
named vector of SNP reference allele frequencies where name is snp id (must match SNP coding used for effect estimates); only needed if Gmat is a covariance matrix and MUST be in same order ans snps in covariance matrix |

list containing the main input for flashfm

Jenn Asimit

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