rvHPDT: Calling haplotype-based and variant-based pedigree disequilibrium test for rare variants in pedigrees.
Version 3.0

To detecting rare variants for binary traits using general pedigrees, the pedigree disequilibrium tests are proposed by collapsing rare haplotypes/variants with/without weights. To run the test, MERLIN is needed in Linux for haplotyping.

Browse man pages Browse package API and functions Browse package files

AuthorWei Guo <wei.guo3@nih.gov>
Date of publication2014-05-14 17:15:23
MaintainerWei Guo <wei.guo3@nih.gov>
LicenseGPL (>= 2)
Version3.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rvHPDT")

Man pages

convert.factors.to.strings.in.dataframe: Convert data.frame columns from factors to characters
fullPedigree: Internal function.
HapMendlianCheck: Internal function.
mydaoshu: Internal function.
mypaste: Internal function.
randomPDT: Internal function.
rchild: Internal function.
rhapPDT: Calling haplotype-based and variant-based pedigree...
rvPDT.test: Variants-based pedigree disequilibrium test for rare variants...
rvPDT.test.permu: Variants-based pedigree disequilibrium test for rare variants...
rvPDT.test.sub: Internal function.
whap.prehap: Prepare haplotype pairs for hPDT tests in pedigree data.

Functions

HapMendlianCheck Man page
convert.factors.to.strings.in.dataframe Man page
fullPedigree Man page
mydaoshu Man page
mypaste Man page
randomPDT Man page Source code
rchild Man page
rhapPDT Man page
rvPDT.test Man page
rvPDT.test.permu Man page
rvPDT.test.sub Man page
whap.prehap Man page

Files

inst
inst/extdata
inst/extdata/example.map
inst/extdata/example.ped
inst/doc
inst/doc/Instruction.txt
NAMESPACE
R
R/hPDT_functions.R
MD5
DESCRIPTION
man
man/rvPDT.test.sub.Rd
man/rhapPDT.Rd
man/rvPDT.test.permu.Rd
man/mypaste.Rd
man/randomPDT.Rd
man/mydaoshu.Rd
man/rchild.Rd
man/HapMendlianCheck.Rd
man/whap.prehap.Rd
man/convert.factors.to.strings.in.dataframe.Rd
man/rvPDT.test.Rd
man/fullPedigree.Rd
rvHPDT documentation built on May 29, 2017, 6:06 p.m.