SummarySeq: Summarise Sequoia Output or Pedigree

In sequoia: Pedigree Inference from SNPs

Summarise Sequoia Output or Pedigree

Description

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.

See Also

sequoia for pedigree reconstruction and links to other functions.

Examples

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

sequoia documentation built on Sept. 8, 2023, 5:29 p.m.