Description Usage Arguments Value

Make two sets of SNP groups using fine-mapping information from all of the traits using two sets of results and maps the names between them

1 2 3 4 5 6 7 8 | ```
makeSNPgroups2(
main.input,
fm.multi,
is.snpmat,
min.mppi = 0.01,
minsnpmppi = 0.001,
r2.minmerge = 0.5
)
``` |

`main.input` |
output from flashfm.input function |

`fm.multi` |
output from flashfm function |

`is.snpmat` |
logical taking value TRUE when genotype matrix is provided and FALSE when covariance matrix is given |

`min.mppi` |
trim snp groups with total MPPI < min.mppi in all diseases; default 0.01 |

`minsnpmppi` |
only group snps with total MPPI > minsnpmppi; default 0.001 |

`r2.minmerge` |
merge groups with minimum between-group r2 > r2.minmerge; default 0.5 |

list of three objects: groups.fm is a list of SNP groups using the single-trait results; groups.flashfm is a list of SNP groups using the flashfm results; group.sizes is a table of SNP group sizes for the two sets of groups

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