Description Usage Arguments Details Value Author(s) References See Also Examples

Performs the Expectation Maximimization Likelihood Ratio Test (EMLRT) proposed by Weinberg (1999) for each SNP in a matrix in genotype format.

1 2 3 4 5 |

`mat.snp` |
a numeric matrix in which each column represents a SNP. Each column must be
a numeric vector of length |

`model` |
a character string specifying the genetic effect that should be considered in the Poisson regression.
By default, the general model proposed by Weinberg (1999) is fitted.
Alternatively, a dominant or recessive mode of inheritance might be considered by setting |

`maternal` |
logical specifying whether parameters for a maternal effects should be added to the Poisson regression model.
If |

`parentMissing` |
a character string specifying whether the genotype of the |

`iter` |
a non-negative numeric value specifying the maximum number of iterations that should be used in the application of the expectation maximization algorithm. |

`eps` |
a non-negative small numeric value specifying the accuracy for the stopping criterion of the EM algorithm.
If the sum of the squared differences of the estimated expected numbers of trios over the 15 possible genotype combinations
in trios between two consecutive iterations of the EM algorithm is smaller than |

`x` |
an object of class |

`digits` |
number of digits that should be printed. |

`top` |
number of SNPs that should be printed. If |

`...` |
ignored. |

While in functions such as `colTDT`

all trios in which the genotype of one or more of the members of this trio
is missing for a particular SNP are removed from the analysis of this SNP, the procedure proposed by Weinberg (1999) can handle missing
genotypes by employing an expectation maximization (EM) algorithm to estimate the expected numbers of
trios for the 15 different genotype combinations
possible in a trio (when considering the genotypes of mothers and fathers individually) and a likelihood ratio test based
on two nested Poisson regression models using the estimated expected numbers of trios as outcome.

An object of class `colEMlrt`

consisting of the following numeric vectors:

`stat` |
the values of the test statistic of the likelihood ratio test for all SNPs in |

`pval` |
the corresponding p-values, |

`ll.full` |
the values of the maximized likelihoods of the full models, |

`ll,red` |
the values of the maximied likelihoods of the reduced models not containing the
parameter(s) corresponding to the genetic |

Philipp Berger, philipp.berger@hhu.de

Weinberg, C.R. (1999). Allowing for Missing Parents in Genetic Studies of Case-Parent Triads.
*American Journal of Human Genetics*, 64, 1186-1193.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
# Load the simulated data.
data(trio.data)
# The EM Likelihood Ratio Test can be applied
# to the SNPs in mat.test by
em.out <- colEMlrt(mat.test)
# If a dominant mode of inheritance is of interest,
# the corresponding EM Likelihood Ratio Test can be
# performed by
emd.out <- colEMlrt(mat.test, model="dominant")
# By default, statistics for the top 5 SNPs are displayed.
# If another number of SNPs, say 10, should be displayed,
# then this can be done by
print(em.out, top = 10)
# The statistics for all SNPs (not ordered by their
# significance) can be obtained by
print(em.out, top = 0)
``` |

trio documentation built on Nov. 8, 2020, 7:41 p.m.

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