| whap.prehap {rvHPDT} | R Documentation |
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).