alleHap (version 0.9.9)

alleHaplotyper: Haplotyping of a dataset composed by several families.

Description

By analyzing all possible combinations of a parent-offspring pedigree in which parents may be missing (missParProb>0), as long as one child was genotyped, it is possible an unequivocal reconstruction of many parental haplotypes. When neither parent was genotyped (missParProb==1), also it is possible to reconstruct at least two parental haplotypes in certain cases. Regarding offspring haplotypes, if both parents are completely genotyped (missParProb==0), in majority of cases partial offspring haplotypes may be successfully obtained (missOffProb>0).

Usage

alleHaplotyper(data, NAsymbol = "?", alleSep = "", invisibleOutput = TRUE,
  dataSummary = TRUE)

Arguments

data

Data containing non-genetic and genetic information of families (or PED file path).

NAsymbol

Icon which will be placed in the NA values of the haplotypes.

alleSep

Icon which will be used as separator of the haplotype alleles.

invisibleOutput

Data are not shown by default.

dataSummary

A summary of the data is shown by default.

Value

Re-imputed alleles and haplotypes for each loaded family.

References

Medina-Rodriguez, N. Santana A. et al. (2014) alleHap: an efficient algorithm to reconstruct zero-recombinant haplotypes from parent-offspring pedigrees. BMC Bioinformatics, 15, A6 (S-3).

Examples

# NOT RUN {
## Haplotype reconstruction for 3 families without missing data.
simulatedFams <- alleSimulator(3,3,6)  
(famsAlls <- simulatedFams[[1]])      # Original data 
famsList <- alleHaplotyper(famsAlls)  # List containing families' alleles and haplotypes
famsList$reImputedAlls                # Re-imputed alleles
famsList$haplotypes                   # Reconstructed haplotypes

## Haplotype reconstruction of a family containing missing data in a parent. 
infoFam <- data.frame(famID="FAM002",indID=1:6,patID=c(0,0,1,1,1,1),
                     matID=c(0,0,2,2,2,2),sex=c(1,2,1,2,1,2),phenot=c(2,1,1,2,1,2))
Mkrs <- rbind(c(1,4,2,5,3,6),rep(NA,6),c(1,7,2,3,3,2),
              c(4,7,5,3,6,2),c(1,1,2,2,3,3),c(1,4,2,5,3,6))
colnames(Mkrs) <- c("Mk1_1","Mk1_2","Mk2_1","Mk2_2","Mk3_1","Mk3_2")
(family <- cbind(infoFam,Mkrs))    # Original data 
famList <- alleHaplotyper(family)  # List containing family's alleles and haplotypes
famList$reImputedAlls              # Re-imputed alleles
famList$haplotypes                 # Reconstructed haplotypes

## Haplotype reconstruction from a PED file
pedFamPath <- file.path(find.package("alleHap"), "examples", "example3.ped") # PED file path
pedFamAlls <- alleLoader(pedFamPath,dataSummary=FALSE) 
pedFamList <- alleHaplotyper(pedFamAlls)
pedFamAlls                # Original data 
pedFamList$reImputedAlls  # Re-imputed alleles 
pedFamList$haplotypes     # Reconstructed haplotypes

# }