Summarise Sequoia Output or Pedigree

Number of assigned parents and grandparents and sibship sizes, split by genotyped, dummy, and 'observed'.

Usage

SummarySeq(
  SeqList = NULL,
  Pedigree = NULL,
  DumPrefix = c("F0", "M0"),
  SNPd = NULL,
  Plot = TRUE,
  Panels = "all"
)

Arguments

SeqList: the list returned by sequoia. Only elements 'Pedigree' or 'PedigreePar' and 'AgePriors' are used. All ids in 'PedigreePar', and only those, are presumed genotyped.
Pedigree: dataframe, pedigree with the first three columns being id - dam - sire. Column names are ignored, as are additional columns, except for columns OHdam, OHsire, MEpair, LLRdam, LLRsire, LLRpair (plotting only).
DumPrefix: character vector of length 2 with prefixes for dummy dams (mothers) and sires (fathers). Will be read from SeqList's 'Specs' if provided. Used to distinguish between dummies and non-dummies. Length 3 in case of hermaphrodites.
SNPd: character vector with ids of SNP genotyped individuals. Only used when Pedigree is provided instead of SeqList, to distinguish between genetically assigned parents and 'observed' parents (e.g. observed in the field, or assigned previously using microsatellites). If NULL (the default), all parents are presumed observed.
Plot: show barplots and histograms of the results, as well as of the parental LLRs, Mendelian errors, and agepriors, if present.
Panels: character vector with panel(s) to plot. Choose from 'all', 'G.parents' (parents of genotyped individuals), 'D.parents' (parents of dummy individuals), 'sibships' (distribution of sibship sizes), 'LLR' (log10-likelihood ratio parent/otherwise related), 'OH' (count of opposite homozygote SNPs).

Value

A list with the following elements:

PedSummary

a 2-column matrix with basic summary statistics, similar to what used to be returned by Pedantics' pedStatSummary (now archived on CRAN). First column refers to the complete pedigree, second column to SNP-genotyped individuals only. Maternal siblings sharing a dummy parent are counted in the 2nd column if both sibs are genotyped, but not if one of the sibs is a dummy individual.

ParentCount

an array with the number of assigned parents, split by:

offspringCat: Genotyped, Dummy, or Observed* (*: only when Pedigree is provided rather than SeqList, for ids which are not listed in SNPd and do not conform to DumPrefix + number (i.e. (almost) al individuals when SNPd = NULL, the default).
offspringSex: Female, Male, Unknown, or Herm* (*: hermaphrodite, only if any individuals occur as both dam and sire). Based only on whether an individual occurs as Dam or Sire.
parentSex: Dam or Sire
parentCat: Genotyped, Dummy, Observed*, or None (*: as for offspringCat)

GPCount

an array with the number of assigned grandparents, split by:

offspringCat: Genotyped, Dummy, Observed*, or All
grandparent kind: maternal grandmothers (MGM), maternal grandfathers (MGF), paternal grandmothers (PGM), paternal grandfathers (PGF)
grandparentCat: Genotyped, Dummy, Observed*, or None

SibSize

a list with elements 'mat' (maternal half + full siblings), 'pat' (paternal half + full siblings), and 'full' (full siblings). Each is a matrix with a number of rows equal to the maximum sibship size, and 3 columns, splitting by the type of parent: Genotyped, Dummy, or Observed.

Examples

SummarySeq(Ped_griffin)

#> ℹ No `OH` panel, because no OH columns
#> SummarySeq: Plotting area too small, or other plotting problem

sumry_grif <- SummarySeq(SeqOUT_griffin, Panels=c("G.parents", "OH"))


sumry_grif$PedSummary
#>                        All SNPd
#> records                167  142
#> maternities            122   65
#> paternities            116   79
#> full sibs                5    5
#> maternal half sib      129   89
#> paternal half sibs     103   77
#> maternal grandmothers   89   77
#> maternal grandfathers   84   75
#> paternal grandmothers   69   58
#> paternal grandfathers   66   55
#> maximum pedigree depth   8    7
#> founders                36   39

Usage

Arguments

Value

See also

Examples