PedCompare {sequoia} | R Documentation

## Compare two Pedigrees

### Description

Compare an inferred pedigree (Ped2) to a previous or simulated pedigree (Ped1), including comparison of sibship clusters and sibship grandparents.

### Usage

    PedCompare(Ped1 = NULL, Ped2 = NULL, na1 = c(NA, "0"),
      DumPrefix = c("F0", "M0"), SNPd = NULL)

### Arguments

`Ped1` | original pedigree, dataframe with columns id-dam-sire; only the first 3 columns will be used.
`Ped2` | infered pedigree, e.g. `SeqOUT$Pedigree`, with columns id-dam-sire.
`na1` | the value for missing parents in Ped1 (assumed NA in Ped2).
`DumPrefix` | character vector of length 2 with the dummy prefices in Pedigree 2; all IDs not starting with the Dummy prefix are taken as genotyped.
`SNPd` | character vector with IDs of genotyped individuals.

### Details

The comparison is divided into different classes of ‘assignable’ parents. This includes cases where the focal individual and parent according to Ped1 are both Genotyped (G-G), as well as cases where the non-genotyped parent according to Ped1 can be lined up with a sibship Dummy parent in Ped2 (G-D), or where the non-genotyped focal individual in Ped1 can be matched to a dummy individual in Ped2 (D-G and D-D). If SNPd is NULL (the default), and DumPrefix is set to NULL, the intersect between the IDs in Pedigrees 1 and 2 is taken as the vector of genotyped individuals.

### Value

A list with

`Counts` | A 7 x 5 x 2 named numeric array with the number of matches and mismatches
`MergedPed` | A side-by-side comparison of the two pedigrees
`ConsensusPed` | A consensus pedigree, with Pedigree 2 taking priority over Pedigree 1
`DummyMatch` | Dataframe with all dummy IDs in Pedigree 2 (id), and the best-matching individual in Pedigree 1 (id.r)
`Mismatch` | A subset of MergedPed with mismatches between Ped1 and Ped2, as defined below. The two additional columns are Cat (category, 'GG', 'GD', 'DG' or 'DD', as described below) and Parent ('dam' or 'sire' indicating which is mismatching)
`Ped1only` | as Mismatches, with parents in Ped1 that were not assigned in Ped2
`Ped2only` | as Mismatches, with parents in Ped2 that were missing in Ped1

The first dimension of `Counts` denotes the following categories:

`GG` | Genotyped individual, assigned a genotyped parent in either pedigree
`GD` | Genotyped individual, assigned a dummy parent, or at least 1 genotyped sibling or a genotyped grandparent in Pedigree 1)
`GT` | Genotyped individual, total
`DG` | Dummy individual, assigned a genotyped parent (i.e., grandparent of the sibship in Pedigree 2)
`DD` | Dummy individual, assigned a dummy parent (i.e., avuncular relationship between sibships in Pedigree 2)
`DT` | Dummy total
`TT` | Total total, includes all genotyped individuals, plus non-genotyped individuals in Pedigree 1, plus non-replaced dummy individuals (see below) in Pedigree 2

The dummy individual count includes all non-genotyped individuals in Pedigree 1 who have, according to either pedigree, at least 2 genotyped offspring, or at least one genotyped offspring and a genotyped parent.

The second dimension of `Counts` gives the outcomes:

`Total` | The total number of individuals with a parent assigned in either or both pedigrees
`Match` | The same parent is assigned in both pedigrees (non-missing). For dummy parents, it is considered a match if the inferred sibship which contains the most offspring of a non-genotyped parent, consists for more than half of this individual's offspring.
`Mismatch` | Different parents assigned in the two pedigrees. When a sibship according to Pedigree 1 is split over two sibships in Pedigree 2, the smaller fraction is included in the count here.
`P1only` | Parent in Pedigree 1 but not 2; includes non-assignable parents (e.g. not genotyped and no genotyped offspring).
`P2only` | Parent in Pedigree 2 but not 1.

The third dimension `Counts` separates between maternal and paternal assignments, where e.g. paternal 'DR' is the assignment of fathers to both maternal and paternal sibships.

'MergedPed' provides the following columns:

`id` | All ids in both Pedigree 1 and 2
`dam.1, sire.1` | parents in Pedigree 1
`dam.2, sire.2` | parents in Pedigree 2
`id.r, dam.r, sire.r` | when in Pedigree 2 a dummy parent is assigned, this column gives the best-matching non-genotyped individual according to Pedigree 1, or "nomatch". If a sibship in Pedigree 1 is divided over 2 sibships in Pedigree 2, the smaller one will be denoted as "nomatch"

In 'ConsensusPed', the priority used is parent.r (if not "nomatch) > parent.2 > parent.1. The columns 'dam.cat' and 'sire.cat' give a 2-letter code denoting whether the focal individual (first letter) and its assigned parent (2nd letter) are

`G` | Genotyped
`D` | Dummy individual (in Pedigree 2)
`R` | Dummy individual in pedigree 2 replaced by best matching non-genotyped individual in pedigree 1
`U` | Ungenotyped (in Pedigree 1, with no dummy match)
`X` | No parent in either pedigree

### Author(s)

Jisca Huisman, jisca.huisman@gmail.com

### See Also

`DyadCompare, sequoia, EstConf`.

### Examples

    ## Not run:
    data(Ped_HSg5, SimGeno_example, LH_HSg5, package="sequoia")
    SeqOUT <- sequoia(GenoM = SimGeno_example, LifeHistData = LH_HSg5)
    compare <- PedCompare(Ped1=Ped_HSg5, Ped2=SeqOUT$Pedigree)
    compare$Counts   # 2 mismatches, due to simulated genotyping errors
    head(compare$MergedPed)

    PedM <- compare$MergedPed
    # find mismatching mothers:
    with(PedM, PedM[which(dam.1!=dam.2 & dam.1!=dam.r),])

    # find mothers in Ped1 which are genotyped but not assigned in Ped2:
    with(PedM, PedM[which(is.na(dam.2) & !is.na(dam.1) &
                           !is.na(id) & dam.1 %in% id),])

    ## End(Not run)

[Package sequoia version 1.3.3 Index]