getPooledGeno {SIMplyBee}

Get a pooled genotype from true genotypes

Description

Level 0 function that returns a pooled genotype from true genotypes to mimic genotyping of a pool of colony members.

Usage

getPooledGeno(x, type = NULL, sex = NULL)

Arguments

x

matrix, true genotypes with individuals in rows and sites in columns

type

character, "mean" for average genotype or "count" for the counts of reference and alternative alleles

sex

character, vector of "F" and "M" to denote the sex of individuals in x

Value

a numeric vector with average allele dosage when type = "mean" and a two-row matrix with the counts of reference (1st row) and alternative (2nd row) alleles

Examples

founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 50)
SP <- SimParamBee$new(founderGenomes)

basePop <- createVirginQueens(founderGenomes)
drones <- createDrones(x = basePop[1], nInd = 1000)
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)
apiary <- createMultiColony(basePop[2:3], n = 2)
apiary <- cross(x = apiary, drones = droneGroups[c(2, 3)])
apiary <- buildUp(x = apiary, nWorkers = 6, nDrones = 3)
apiary <- addVirginQueens(x = apiary, nInd = 5)

genoQ <- getQueenSegSiteGeno(apiary[[1]])
genoF <- getFathersSegSiteGeno(apiary[[1]])
genoW <- getWorkersSegSiteGeno(apiary[[1]])
genoD <- getDronesSegSiteGeno(apiary[[1]])
genoV <- getVirginQueensSegSiteGeno(apiary[[1]])

# Pool of drones
sexD <- getCasteSex(apiary[[1]], caste = "drones")
getPooledGeno(x = genoD, type = "count", sex = sexD)[, 1:10]
(poolD <- getPooledGeno(x = genoD, type = "mean", sex = sexD))[, 1:10]
# ... compare to queen's genotype
genoQ[, 1:10]
plot(
  y = poolD, x = genoQ, ylim = c(0, 2), xlim = c(0, 2),
  ylab = "Average allele dosage in drones",
  xlab = "Allele dosage in the queen"
)

# As an exercise you could repeat the above with different numbers of drones!

# Pool of workers
getPooledGeno(x = genoW, type = "count")[, 1:10]
(poolW <- getPooledGeno(x = genoW, type = "mean"))[, 1:10]
# ... compare to fathers' and queen's avearage genotype
sexF <- getCasteSex(apiary[[1]], caste = "fathers")
sexQ <- rep(x = "F", times = nrow(genoF))
sexFQ <- c(sexF, sexQ)
genoFQ <- rbind(genoF, genoQ[rep(x = 1, times = nrow(genoF)), ])
(poolFQ <- getPooledGeno(x = genoFQ, type = "mean", sex = sexFQ))[, 1:10]
plot(
  y = poolW, x = poolFQ, ylim = c(0, 2), xlim = c(0, 2),
  ylab = "Average allele dosage in workers",
  xlab = "Average allele dosage in the queen and fathers"
)

# As an exercise you could repeat the above with different numbers of workers!