Description Usage Arguments Details Value See Also Examples

Functions to read in and use MangroveORs objects

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`ORfile` |
The location of an odds ratio file to read in |

`header` |
Logical. Indicates whether the ORfile above has a header. |

`x` |
A |

`object` |
A |

`K` |
The prevalence of the disease that the odds ratios predict. If NULL, data is returned for a few example prevalences. |

`...` |
Additional arguments to be passed to downstream methods. |

A `MangroveORs`

object is used to hold the risk alleles, odds ratios and frequencies for a set of genetic variants used to predict disease. You can read an odds ratio file from disk using `readORs`

.

The format of the odds ratio file is a text file with 4 or 5 columns. If the file has 4 columns, the first should be the variant ID, the second the risk allele, the third the additive odds ratio and the fourth the frequency. If 5 columns exist, column three is the heterozygous odds ratio, column four is the homozygous risk odds ratio, and five is the allele frequency.

The `print`

method shows the data that the object holds. The `summary`

method gives some measures of how predictive the variants are, including the variance explained by the variants in the object on the liability scale. The `plot`

method show the cumulative variance explained on the liability scale as the variants are added in one-at-a-time (in order of most-to-least variance explained).

See `vignette("Mangrove")`

for an example of an odds ratio file, and usage of an odds ratio object.

An object of class `MangroveORs`

for `readORs`

. Nothing is returned for the methods.

`MangroveRiskPreds`

for performing risk prediction using this object, and `getVarExp`

for more on assessing variance explained.

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Mangrove documentation built on May 29, 2017, 11:54 a.m.

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