rvHPDT (version 3.0)

rhapPDT: Calling haplotype-based and variant-based pedigree disequilibrium test for rare variants in pedigrees.

Description

To detecting rare variants for binary traits using general pedigrees, the pedigree disequilibrium tests are proposed by collapsing rare haplotypes/variants with/without weights.

Usage

rhapPDT(ped, map, aff=2, unaff=1, mu=1.04,
merlinFN.prefix="merlin", nperm=1000, trace=TRUE)

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.

aff

indicates the values that represents affected status in "PHENO" column of PED data; default is 2.

unaff

indicates the values that represents unaffected status in "PHENO" column of PED data; default is 1.

mu

indicates mu value that defines causal in the training data; default is 1.04.

merlinFN.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.

nperm

indicates the times of permutation; default is 1000.

trace

Indicates whether or not the intermediate outcomes should be printed; default is FALSE.

Value

hPDT_v0

P value of unweighted haplotype PDT test statistic.

hPDT_v1

P value of weighted haplotype PDT test statistic.

rvPDT_v0

P value of unweighted rvPDT test statistic.

rvPDT_v1

P value of weighted rvPDT test statistic.

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).

Examples

# NOT RUN {
#ped<-read.table("MLIP.ped",head=1,stringsAsFactors=FALSE)
#map<-read.table("MLIP.map",head=1,stringsAsFactors=FALSE)  
#test<-rhapPDT(ped, map, trace=TRUE) 
#test 
#$hPDT_v0
#[1] 0.4231359

#$hPDT_v1
#[1] 0.1481145

#$rvPDT_v0
#[1] 0.03237073

#$rvPDT_v1
#[1] 0.162997
# }