ribd (version 1.1.0)

twoLocusPlot: Two-locus coefficient plot

Description

Plot two-locus kinship or IBD coefficients as function of the recombination rate.

Usage

twoLocusPlot(
  peds,
  coeff = "k11",
  xlab = "Recombination rate",
  ylab = NA,
  col = seq_along(peds),
  lty = 1,
  ...
)

Arguments

peds

A list of lists. See details.

coeff

A string identifying which coefficient to compute. See Details for legal values.

xlab, ylab, col, lty

Plotting parameters

...

Further parameters passed on to matplot()

Details

Each entry of peds must be a list with the following (named) entries:

• ped: A ped object

• ids: A pair of labels identifying two members of ped

The coeff parameter must be either a character naming the coefficient to compute, or a function. If a character, it must be one of the following names: "kinship", "phi", "phi11", "k00", "k01", "k02", "k10", "k11", "k12", "k20", "k21" or "k22".

If coeff is a function, it must take three arguments named ped, ids and rho, and produce a single number for each set of input data. See Examples.

The first three are synonymous and indicate the two-locus kinship coefficient. The remaining choices are two-locus IBD coefficients. (See twoLocusIBD().)

Examples

# NOT RUN {
###############################
# Classic example of three relationships with equal one-locus coeffs
peds = list(
    GrandParent = list(ped = linearPed(2),    ids = c(1, 5)),
    HalfSib     = list(ped = halfSibPed(),    ids = c(4, 5)),
    Uncle       = list(ped = cousinPed(0, 1), ids = c(3, 6)))

twoLocusPlot(peds, coeff = "kinship")
twoLocusPlot(peds, coeff = "k11")

###############################

peds = list(
    PO = list(ped = nuclearPed(1), ids = c(1,3)),
    S  = list(ped = nuclearPed(2), ids = c(3,4)))

twoLocusPlot(peds, coeff = "kinship")
twoLocusPlot(peds, coeff = "k11")

###############################

peds = list(
   `H-sibs` = list(ped = addChildren(halfSibPed(sex2 = 2), 4, 5, nch = 2),
                 ids = 6:7),
   `G-sibs` = list(ped = addChildren(addDaughter(nuclearPed(1), 3), 1, 5, nch = 2),
                 ids = 6:7),
   `U-sibs` = list(ped = addChildren(addDaughter(nuclearPed(2), 4), 3, 6, nch = 2),
                 ids = 7:8)
)
# plotPedList(peds)
twoLocusPlot(peds, coeff = "kinship")

################################

### Example where `coeff` is a function.
### Reproducing Fig 2 of Bishop & Williamson (1990)

# The coefficient d11(rho) is the conditional probability of IBD = 1
# in the first locus, given IBD = 1 in the second.

peds = list(
    GrandParent = list(ped = linearPed(2),    ids = c(1, 5)),
    HalfSib     = list(ped = halfSibPed(),    ids = c(4, 5)),
    Uncle       = list(ped = cousinPed(0, 1), ids = c(3, 6)),
    FirstCous   = list(ped = cousinPed(1),    ids = c(5, 8)),
    FirstCous1R = list(ped = cousinPed(1, 1), ids = c(5, 10)),
    SecondCous  = list(ped = cousinPed(2),    ids = c(7, 12)))

d11 = function(ped, ids, rho) {
  twoLocusIBD(ped, ids, rho, coefs = "k11")/kappaIBD(ped, ids)[2]
}

twoLocusPlot(peds, coeff = d11)

# }