rvPDT.test.permu | R Documentation |
To detecting rare variants for binary traits using general pedigrees, the pedigree disequilibrium tests are extended by collapsing rare variants with/without weights.
rvPDT.test.permu(ped, aff=2,unaff=1, snpCol, hfreq=NULL, useFamWeight=TRUE, nperm=1000,trace=FALSE)
ped |
input data, has same format with PLINK but having column names. The PED file is a white-space (space or tab) delimited file: 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. |
aff |
indicates the values that represents affected status in ped data; default is 2. |
unaff |
indicates the values that represents unaffected status in ped data; default is 1. |
snpCol |
indicates the columns of variants in ped data. |
hfreq |
indicates the frequencies of variants that used in calculating weights; when it is NULL, the frequencies are estimated by ped data. |
useFamWeight |
indicates whether the family weights need to be used in the test. |
nperm |
indicates the times of permutation; default is 1000. |
trace |
indicates wether or not the intermediate outcomes should be printed; default is FALSE. |
TDT |
Transmission/disequilibrium matrix for each pedigrees. |
Sib |
Discordant sib pairs matrix for each pedigrees. |
PDT |
Pedigree disequilibrium matrix for each pedigrees, which is the sum of TDT and Sib. |
W |
Weights used in Weighted rvPDT test. |
test.v1 |
Weighted rvPDT test statistic with weights W. |
test.v0 |
Unweighted rvPDT test statistic with weights=1. |
pvalue.v1 |
P value of weighted rvPDT test statistic (test.v1). |
pvalue.v0 |
P value of unweighted rvPDT test statistic (test.v0). |
Guo W , Shugart YY, Does Haplotype-based Collapsing Tests Gain More Power than Variant-based Collapsing Tests for Detecting Rare Variants in Pedigrees (manuscript).
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