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

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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.

Author
Wei Guo <wei.guo3@nih.gov>
Date of publication
2014-05-14 17:15:23
Maintainer
Wei Guo <wei.guo3@nih.gov>
License
GPL (>= 2)
Version
3.0

View on CRAN

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.

Files in this package

rvHPDT
rvHPDT/inst
rvHPDT/inst/extdata
rvHPDT/inst/extdata/example.map
rvHPDT/inst/extdata/example.ped
rvHPDT/inst/doc
rvHPDT/inst/doc/Instruction.txt
rvHPDT/NAMESPACE
rvHPDT/R
rvHPDT/R/hPDT_functions.R
rvHPDT/MD5
rvHPDT/DESCRIPTION
rvHPDT/man
rvHPDT/man/rvPDT.test.sub.Rd
rvHPDT/man/rhapPDT.Rd
rvHPDT/man/rvPDT.test.permu.Rd
rvHPDT/man/mypaste.Rd
rvHPDT/man/randomPDT.Rd
rvHPDT/man/mydaoshu.Rd
rvHPDT/man/rchild.Rd
rvHPDT/man/HapMendlianCheck.Rd
rvHPDT/man/whap.prehap.Rd
rvHPDT/man/convert.factors.to.strings.in.dataframe.Rd
rvHPDT/man/rvPDT.test.Rd
rvHPDT/man/fullPedigree.Rd