hapassoc (version 0.1)

RecodeHaplos: Recode SNP genotype data into possible haplotypes

Description

This function takes as an argument the original data frame with non-SNP and SNP data and converts the genotype data at single SNPs (the single-locus genotypes) into haplotype data. The rows of the original data frame should correspond to subjects and each SNP should have two columns, one for each allele of the single-locus genotype. The SNP data should comprise the last 2*numSNPs columns. If the haplotypes for a subject cannot be inferred from his or her genotype data, "pseudo-individuals" representing all possible haplotype combinations consistent with the single-locus genotypes are considered. Missing single-locus genotypes, up to a maximum of maxMissingGenos (see below), are allowed, but subjects with missing data in more than maxMissingGenos, or with missing non-SNP data, are removed.

Usage

RecodeHaplos(dat, numSNPs, maxMissingGenos = 1)

Arguments

dat

the non-SNP and SNP data as a data frame

numSNPs

the number of SNPs in a haplotype

maxMissingGenos

maximum number of single-locus genotypes with missing data to allow for each subject. (Subjects with more missing data, or with missing non-SNP data are removed.) The default is 1.

Value

• nonHaploDM
  non-genetic portion of an AUGMENTED data frame which includes any possible pseudo-individuals
• haploDM
  a data frame with $2^{numSNPs}$ columns scoring number of copies of each haplotype for each pseudo-individual
• haploMat
  matrix with 2 columns giving the haplotypes as a string of zeros and ones for each pseudo-individual
• wt
  vector of crude weights for each pseudo-individual to be updated by CheckHaplos
• ID
  index for each individual in the original data frame. Note that all pseudo-individuals for a subject have the same ID value

synopsis

RecodeHaplos(dat, numSNPs, maxMissingGenos = 1, logriskmodel="additive")

See Also

CheckHaplos,EM,summary.EM.

Examples

# To convert SNP data from a simulated diabetes example into two-locus haplotypes:
data(hypoDat)
example.haplos<-RecodeHaplos(hypoDat, 2)