Description Usage Arguments Details Value Note See Also Examples

The function makes each pair of columns a locus object, which recodes alleles to numeric and saves the original alleles as an attribute of the model.matrix.

1 |

`geno` |
Matrix of alleles, such that each locus has a pair of adjacent columns of alleles, and the order of columns corresponds to the order of loci on a chromosome. If there are K loci, then ncol(geno) = 2*K. Rows represent alleles for each subject. |

`miss.val ` |
A vector of codes denoting missing values for allele1 and allele2. Note that NA will always be treated as a missing value, even if not specified in miss.val. Also note that if multiple missing value codes are specified, the original missing value code for a specific individual can not be retrieved from the loci object. |

`locus.label` |
vector of labels for the loci |

This function contains the essential parts of the loci function, which is no longer within haplo.stats

A 'model.matrix' object with the alleles recoded to numeric values, and the original values are stored in the 'unique.alleles' attribute. The ith item of the unique.alleles list is a vector of unique alleles for the ith locus.

A matrix that contains all elements of mode character will be sorted
in alphabetic order. This order may differ across platforms according
to your setting of LC_COLLATE. See the note in `haplo.em`

about
how this sort order affects results.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
# Create some loci to work with
a1 <- 1:6
a2 <- 7:12
b1 <- c("A","A","B","C","E","D")
b2 <-c("A","A","C","E","F","G")
c1 <- c("101","10","115","132","21","112")
c2 <- c("100","101","0","100","21","110")
myGeno <- data.frame(a1,a2,b1,b2,c1,c2)
myGeno <- setupGeno(myGeno)
myGeno
attributes(myGeno)$unique.alleles
``` |

haplo.stats documentation built on May 29, 2017, 7:54 p.m.

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