whap.prehap: Prepare haplotype pairs for hPDT tests in pedigree data.

In rvHPDT: Calling Haplotype-Based and Variant-Based Pedigree Disequilibrium Test for Rare Variants in Pedigrees

Prepare haplotype pairs for hPDT tests in pedigree data.

Description

Before running hPDT test, haplotype pairs are inferred by calling MERLIN in linux for all pedigree members, and then perpare some internal statistics. Require the R package of "gregmisc" and MERLIN software.

Usage

 
whap.prehap(ped,map, merlinDir="", outFN.prefix="merlin",aff=2,trace=FALSE)  

Arguments

ped	input data, has same format with PLINK but having column names. The PED file is a white-space (space or tab) delimited file, and the first six columns are mandatory: FID: Family ID; IID: Individual ID; FA: Paternal ID; MO: Maternal ID; SEX: Sex (1=male; 2=female; other=unknown); PHENO: Phenotype; Genotypes (column 7 onwards) should also be white-space delimited; they are coded as 0, 1 and 2, indicating the number of coding allele, and NA is for missing genotype.
map	input data, has same format with MAP file required by MERLIN. The MAP file is a white-space (space or tab) delimited file with 3 columns as follows, CHROMOSOME: chromosome (1-22, X, Y or 0 if unplaced) MARKER: marker name in PED file that is usually rs# or snp identifier POSITION: Genetic distance (morgans) The data file and map file can include different sets of markers, but markers that are absent from the map file will be ignored by MERLIN.
merlinDir	indicates the directory of Merlin, for example, merlinDir="./Merlin/"; use the default="" when Merlin is in current directory or your bin directory.
outFN.prefix	Requests that output file of MERLIN names should be derived from outFN.prefix. For example, when it is set to be "merlin" as default, estimated haplotypes should be stored in a file called merlin.chr.
aff	indicates the values that represents affected status in ped data; default is 2.
trace	indicates whether or not the intermediate outcomes should be printed; default is FALSE.

Value

SNPname	SNP names of testing.
hapData	Haplotype data for each individuals.
freq	Estimated frequencies of haplotypes.
trans	Transmission matrix of haplotypes.
hapScore	Score matrix of haplotypes.

References

Guo W , Shugart YY, Does Haplotype-based Collapsing Tests Gain More Power than Variant-based Collapsing Tests for Detecting Rare Variants in Pedigrees (manuscript).

rvHPDT documentation built on May 13, 2022, 1:06 a.m.