This is a data frame created by the function ld_lasso_method. It contains information about the parameters used to generate the three LD LASSO solutions, as well as the solutions themselves. It also contains the results from the grid search performed to estimates the cp-optimal solution. (see cp.obj) Some basic map information is also stored here for use when plotting.

1 |

data.frame

beta1 | numeric | cp-optimal solution |

beta2 | numeric | fused solution |

beta3 | numeric | un-fused solution |

s2star | numeric | s2 parameter used for cp-optimal solution |

cp.obj | data.frame | s2 and cp vectors along with solution matrix used to find s2star |

log10p | numeric | log base 10 of p-values from allelic test of association for each SNP |

bpmap | numeric | vector of physical SNP positions in kb from left boundary |

block.bounds.vec | numeric | position of block boundaries in kb from left boundary (does not inlcude endpoints) |

s1 | numeric | LASSO parameter |

B | numeric | number of bootstrap samples used by ld_lasso_method to find s2star |

s2.vec.length | numeric | length of vector of s2 values used in ld_lasso_method |

Samuel Younkin, Joseph Nadeau, Robert Elston and J. Sunil Rao, "The Linkage Disequilibrium LASSO for SNP Selection in a Genetic Association Study of Late Onset Alzheimer Disease," Technical Report, 2010

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