SummarySeq {sequoia} | R Documentation |
Number of assigned parents and grandparents and sibship sizes, split by genotyped, dummy, and 'observed'.
SummarySeq(SeqList = NULL, Ped = NULL, DumPrefix = c("F0", "M0"), SNPd = NULL, Plot = TRUE)
SeqList |
the list returned by |
Ped |
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 |
SNPd |
character vector with ids of SNP genotyped individuals. Only when
|
Plot |
Show barplots and histograms of the results, as well as of the parental LLRs, Mendelian errors, and agepriors, if present. |
A list with the following elements:
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 4x4 matrix with for all genotyped individuals the number of assigned grandparents, split by D1: Maternal grandmother, maternal grandfather, paternal grandmother, paternal grandfather; D2: 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. |
## Not run: data(SimGeno_example, LH_HSg5, package="sequoia") SeqOUT <- sequoia(GenoM = SimGeno_example, LifeHistData = LH_HSg5, MaxSibIter = 10) Ped_example <- SeqOUT$Pedigree Ped_example$dam[1:20] <- paste0("Mum", 1:20) # some field mums SummarySeq(SeqOUT, Ped=Ped_example) ## End(Not run)