Description Usage Arguments Value Examples

The entry point for rolypoly analysis. If no expression data, we assume that we are running just the vegas score processing.

1 2 3 4 5 6 | ```
rolypoly_roll(rolypoly = NULL, gwas_data = NULL, block_annotation = NULL,
block_data = NULL, ld_folder = NULL, bootstrap_iters = 50,
outlier_threshold = -1, perform_cv = F, n_folds = 10,
gwas_z_filter = -1, add_spline = F, n_knots = 1, add_poly = F,
n_degree = 2, run_light = T, gwas_link_parallel = F,
bootstrap_parallel = F, keep_model = F, keep_gwas = F, ...)
``` |

`rolypoly` |
Previous rolypoly run to parts of pipeline. |

`gwas_data` |
Gwas data for a trait, including snp annotations. |

`block_annotation` |
Start and end points for blocks |

`block_data` |
Information about blocks. |

`ld_folder` |
Folder with LD information. |

`bootstrap_iters` |
Number bootstrap iterations to perform for inference. |

`outlier_threshold` |
Set to positive if we want to run robusted regression. |

`perform_cv` |
If we want to interpret annotation effects do not set this to T. However, if our goal is prediction accuracy then set this to T. |

`n_folds` |
number of folds for cross validation |

`gwas_z_filter` |
Z-score filter for SNPs, helps prevent large effects biasing inference. |

`add_spline` |
If we want to fit a spline to maf. |

`n_knots` |
number of knots to add to the spline. |

`add_poly` |
If we want to fit a polynomial to maf. |

`n_degree` |
the degree of the polynomial. |

`run_light` |
if we want to throw away bootstrap data, and save memory |

`gwas_link_parallel` |
if user wants to run in gwas linking in parallel, registerDoParallel must have been run in advance. |

`bootstrap_parallel` |
if user wants to run in bootstraps in parallel, registerDoParallel must have been run in advance. |

`keep_model` |
if we should keep the regression model, can be large. |

`keep_gwas` |
set to T if we want to include gwas in returned rolypoly object. |

`...` |
other arguments to pass to cv.glmnet |

rolypoly object

1 | ```
## Not run: rolypoly_roll(rolypoly)
``` |

```
Welcome to rolypoly! Say hi @diegoisworking.
```

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