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

View source: R/fat2Lpoly.withinR.R

Same as `fat2Lpoly`

except that the first four arguments of `fat2Lpoly`

are replaced by one object having the format of the objects returned by `read.merlin.files`

.

1 2 3 | ```
fat2Lpoly.withinR(ped.x.all, snp.names.mat, ibd.loci = NULL, contingency.file = FALSE,
design.constraint, par.constrained, constraints,
pairweights=calcule.poids.alphafixe, lc = NULL, alpha = NULL)
``` |

`ped.x.all` |
object returned by the function |

`snp.names.mat` |
matrix of one or two columns giving the names of the SNPs (if one column matrix) or pairs of SNPs (if two columns matrix) to be analyzed. These SNPs represent all or part of the SNPs in the data files |

`ibd.loci` |
matrix of the same dimensions as |

`contingency.file` |
if 'TRUE' (default is 'FALSE'), then a file called descriptive_statistics'date_and_time'.txt is created and contingency tables with the numbers of subjects per level are progressively added to this file. |

`design.constraint` |
function building the design matrices WITHIN each category, for constraints specific to each category. It also returns the design matrices comprising only the loci main effects that are used for computing the covariances. |

`par.constrained` |
Optional matrix of dimensions ( |

`constraints` |
Optional matrix of dimensions ( |

`pairweights` |
function calculating the weights of the observation pair differences when conditioning on the first SNP in the test of the second SNP in a SNP pair. Default is calcule.poids.alphafixe, implementing the weighting function of equation (6) of reference [1]. An alternative is calcule.poids.Chen, implementing the weighting function of equation (7) of reference [1]. |

`lc` |
numerical identifier of the SNP (locus) on which to condition when testing model terms. Defaults to NULL, or no conditioning. |

`alpha` |
vector of length |

File "descriptive_statistics'date_and_time'.txt" (will be created if contingency.file='TRUE'): For each tested SNP, it shows contingency tables of the subjects in the 2 or 4 different categories, first for all families together and then for each individual family.

If the argument ibd.loci is left unspecified (or NULL, its default), then we use the kinship coefficients multiplied by two, instead of the expectation of the IBD probabilities, in the computation of the score statistics. The kinship coefficients are obtained using the function `kinship`

from the package `kinship2`

.

`scores.covs.all.SNPs` |
list of length 'nrow( |

`snp.names.mat` |
(same matrix as provided as argument) matrix of one or two columns giving the names of the SNPs (if one column matrix) or pairs of SNPs (if two columns matrix) to be analyzed. These SNPs represent all or part of the SNPs in the data files |

Alexandre Bureau and Jordie Croteau

Bureau A., Croteau J., Chagnon, Y.C., Roy, M.-A. and Maziade, M. Extension of the Generalized Disequilibrium Test to polytomous phenotypes and two locus models. Frontiers in Genetics, 5: Article 258.

`fat2Lpoly, read.merlin.files, get.scores.pvalues`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
data(ped.x.all)
## Not run:
snp.names.mat=cbind(rep("snp4.loc1",2),c("snp3.loc2","snp4.loc2"))
microsat.names.mat=cbind(rep("1_4_mrk:",2),c("2_3_mrk:","2_4_mrk:"))
fat2Lpoly.allSNPs=fat2Lpoly.withinR(ped.x.all,snp.names.mat,ibd.loci=
microsat.names.mat,contingency.file=TRUE,
design.constraint=design.endo2disease,
lc=1)
joint.tests=list(c(2,5))
get.scores.pvalues(fat2Lpoly.allSNPs,joint.tests)
## End(Not run)
``` |

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