sequoia (version 2.3.5)

SummarySeq: 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.

Pedigree

dataframe, pedigree with the first three columns being id - dam - sire. Column names are ignored, as are additional columns.

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 when Pedigree is provided instead of SeqList, then used to distinguish between genetically assigned parents and 'observed' parents (e.g. observed in the field, or assigned previously using microsatellites). If SeqList's 'PedigreePar' is provided, all ids in that dataframe will be presumed genotyped.

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

a 2x3x2x4 array with the number of assigned parents, split by D1: genotyped vs dummy individuals; D2: female, male and unknown-sex individuals; D3: dams vs sires; D4: genotyped, dummy, observed vs no parent

GPCount

a 2x4x4 array with the number of assigned grandparents, split by D1: genotyped vs dummy individuals; D2 Maternal grandmother (MGM), maternal grandfather (MGF), paternal grandmother (PGM), paternal grandfather (PGF); D3: genotyped, dummy, observed vs no grandparent

SibSize

a list with as first element a table of maternal sibship sizes, and as second element a table of paternal sibship sizes. Each table 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

# NOT RUN {
data(SimGeno_example, LH_HSg5, package="sequoia")
SeqOUT <- sequoia(GenoM = SimGeno_example,
                   LifeHistData = LH_HSg5, Module="ped")
Ped_example <- SeqOUT[["Pedigree"]]
Ped_example$dam[1:20] <- paste0("Mum", 1:20)  # some fake field mums
PedSum1 <- SummarySeq(SeqOUT, Pedigree=Ped_example, Panels="G.parents")
summary(PedSum1)
PedSum1$PedSummary
# }
# NOT RUN {
# }