fpederr {pedantics} | R Documentation |
Implements the 'forward' approach to producing pairs of pedigrees for power and sensitivity analyses.
fpederr(truePedigree, founders = NULL, sex = NULL, samp = NULL, sireE = NULL, damE = NULL, sireA = NULL, damA = NULL, cohort = NULL, first = NULL, last = NULL, monoecey = 0, modifyAssumedPedigree = 0)
truePedigree |
A complete pedigree with records for all individuals and parental ID's for all non-founders |
founders |
A vector the same length as the pedigree containing indicator variables 1 = founder, 0 = non-founder |
sex |
A vector the same length as the pedigree indicating sex, 0=male, 1=female, any other value = unknown sex |
samp |
A vector the same length as the pedigree indicating whether or not each individual is sampled (1), or an unsampled dummy individual (0). |
sireE |
Value(s) indicating the paternal error rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals. |
damE |
Value(s) indicating the maternal error rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals. |
sireA |
Value(s) indicating the paternal pedigree link assignment rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals. |
damA |
Value(s) indicating the maternal pedigree link assignment rate. If it is a single number (between 0 and 1), it is applied to the entire pedigree; if it is a vector the length of the pedigree, then probabilities can vary among individuals. |
cohort |
A numeric vector the same length as the pedigree containing cohorts |
first |
A numeric vector the same length as the pedigree indicating the first cohort for which an individual is to be considered a potential parent |
last |
A numeric vector the same length as the pedigree indicating the last cohort for which an individual is to be considered a potential parent |
monoecey |
An indicator specifying whether or not bisexuality is allowed (0=no (default), 1=yes) |
modifyAssumedPedigree |
An indicator variable specifying whether or not an assumed pedigree with errors but no missing links should be supplied. |
assumedPedigree |
A pedigree differing from the supplied pedigree so as to mimic patterns of pedigree errors and missing data that might occur in a real study. |
truePedigree |
Echos the pedigree supplied. |
supplementalPedigree |
(optional) a 'assumed' pedigree containing errorsbut no missing links. |
Michael Morrissey michael.morrissey@ed.ac.uk
Morrissey et al. 2007. Journal of Evolutionary Biology 20:2309-2321., Morrissey, M.B, and A.J. Wilson, 2009. pedantics, an R package for pedigree-based genetic simulation, and pedigree manipulation, characterisation, and viewing. Molecular Ecology Resources.
testData<-as.data.frame(matrix(c( 1, NA, NA, 1, 1, 1, 2, 2, 2, NA, NA, 1, 1, 1, 2, 2, 3, NA, NA, 1, 1, 1, 2, 2, 4, NA, NA, 1, 0, 1, 2, 2, 5, NA, NA, 1, 0, 1, 2, 2, 6, 1, 4, 0, -1, 2, 3, 3, 7, 1, 4, 0, -1, 2, 3, 3, 8, 1, 4, 0, -1, 2, 3, 3, 9, 1, 4, 0, -1, 2, 3, 3, 10, 2, 5, 0, -1, 2, 3, 3, 11, 2, 5, 0, -1, 2, 3, 3, 12, 2, 5, 0, -1, 2, 3, 3, 13, 2, 5, 0, -1, 2, 3, 3, 14, 3, 5, 0, -1, 2, 3, 3, 15, 3, 5, 0, -1, 2, 3, 3, 16, 3, 5, 0, -1, 2, 3, 3, 17, 3, 5, 0, -1, 2, 3, 3), 17,8,byrow=TRUE)) names(testData)<-c("id","dam","sire","founder","sex", "cohort","first","last") pedigree<-as.data.frame(cbind(testData$id,testData$dam, testData$sire)) for(x in 1:3) pedigree[,x]<-as.factor(pedigree[,x]) names(pedigree)<-c("id","dam","sire") pedigree ## some missing sire links: fpederr(truePedigree=pedigree,founders=testData$founder, sex=testData$sex,sireA=0.5,cohort=testData$cohort, first=testData$first,last=testData$last)$assumedPedigree ## some erroneous sire links: fpederr(truePedigree=pedigree,founders=testData$founder, sex=testData$sex,sireE=0.5,cohort=testData$cohort, first=testData$first,last=testData$last)$assumedPedigree