Number of assigned parents and grandparents and sibship sizes, split by genotyped, dummy, and 'observed'.
SummarySeq(
SeqList = NULL,
Pedigree = NULL,
DumPrefix = c("F0", "M0"),
SNPd = NULL,
Plot = TRUE,
Panels = "all"
)A list with the following elements:
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.
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)
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
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.
the list returned by sequoia. Only elements
'Pedigree' or 'PedigreePar' and 'AgePriors' are used. All ids in
'PedigreePar', and only those, are presumed genotyped.
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).
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.
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.
show barplots and histograms of the results, as well as of the parental LLRs, Mendelian errors, and agepriors, if present.
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).
PlotSeqSum to plot the output of this function;
sequoia for pedigree reconstruction and links to other
functions.
SummarySeq(Ped_griffin)
sumry_grif <- SummarySeq(SeqOUT_griffin, Panels=c("G.parents", "OH"))
sumry_grif$PedSummary
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