MCPDT {MCPDT} | R Documentation |
Pedigree disequilibrium test (PDT) and pedigree parental-asymmetry test (PPAT) with missing genotypes simulated conditioned on observed genotypes.
MCPDT(ped,mcsize,loci=NULL,af=NULL,sexlinked=FALSE) MCPPAT(ped,mcsize,loci=NULL,af=NULL,sexlinked=FALSE)
ped |
name of a standard LINKAGE pedigree file (pre-makeped format) or a matrix/dataframe containing the pedigree data |
mcsize |
Monte Carlo sample size |
loci |
name of a standard LINKAGE loci file |
af |
matrix of marker allele frequencies, one column for each marker |
sexlinked |
whether the markers are on X chromosome |
‘MCPDT’ calculates PDT and MCPDT statistics and p-values.
‘MCPPAT’ calculates PDT, MCPDT, PPAT and MCPPAT statistics and p-values.
ped is required. Only SNP markers are supported. If loci file is provided, allele frequencies are read from the file specified. Otherwise, they can be provided directly in the argument af. If allele frequencies are not provided in either way, they are estimated from all the typed founders' genotypes.
If there are multiple markers, each marker is analyzed separately.
sexlinked only applies to MCPDT since MCPPAT only deals with autosomal markers. If sexlinked=TRUE in ‘MCPPAT’, only PDT and MCPDT will be calculated.
Tstat |
PDT T statistics for the markers |
pvalue |
P values assuming asymptotic normal distribution |
mcsize |
Monte Carlo sample size |
af |
allele frequencies used in the simulation |
Martin, E. R., Monks, S. A., Warren, L. L. and Kaplan, N. L. (2000) A test for linkage and association in general pedigrees: the pedigree disequilibrium test. Am J Hum Genet 67:146-154
Ding, J., Lin, S. and Liu, Y. (2006) Monte Carlo pedigree disequilibrium test for markers on the X chromosome. Am J Hum Genet 79:567-573
Zhou, J.Y., Ding, J., Fung, W.K. and Lin, S. (2009) Detection of parent-of-origin effects using general pedigree data. Submitted
Ott, J. (1989) Computer-simulation methods in human linkage analysis. Proc Natl Acad Sci USA 86:4175-4178
Weeks, D. E., Ott, J., and Lathrop, G. M. (1990) SLINK: A general simulation program for linkage analysis. Am J Hum Genet 47:A204