CrypticIBDcheck: Identifying cryptic relatedness in genetic association studies

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Exploratory tools to identify closely related subjects using autosomal genetic marker data.

Author
Annick Joelle Nembot-Simo, Jinko Graham and Brad McNeney
Date of publication
2013-09-21 08:05:29
Maintainer
Brad McNeney <mcneney@sfu.ca>
License
GPL-3
Version
0.3-1

View on CRAN

Man pages

countIBS
calculates counts of 0, 1 and 2 IBS
CrypticIBDcheck-package
identify cryptic relatedness in genetic association studies
filter.control
Set options for quality control filtering of data.
IBD
Constructor function for objects of class 'IBD'
IBDcheck
estimate IBD coefficients to identify cryptic relatedness in...
new.IBD
Create a data structure suitable for input to 'IBDcheck'
Nhlsim
Example data for the CrypticIBDcheck package
plot.IBD
plot estimated IBD coefficients for pairs of study subjects,...
RutgersMapB36
physical and genetic map positions for a collection of...
sim.control
Set options that control gene drop simulation of relationship...
SNPgenmap
convert physical map positions on build 36 of the genome to...

Files in this package

CrypticIBDcheck
CrypticIBDcheck/inst
CrypticIBDcheck/inst/CITATION
CrypticIBDcheck/inst/scripts
CrypticIBDcheck/inst/scripts/thin.R
CrypticIBDcheck/inst/doc
CrypticIBDcheck/inst/doc/IBDcheck-hapmap.pdf
CrypticIBDcheck/inst/doc/CrypticIBDcheck.Rnw
CrypticIBDcheck/inst/doc/IBDcheck-hapmap.Rnw
CrypticIBDcheck/inst/doc/IBDcheck-hapmap.R
CrypticIBDcheck/inst/doc/CrypticIBDcheck.pdf
CrypticIBDcheck/src
CrypticIBDcheck/src/IBDestp.c
CrypticIBDcheck/src/countIBS.c
CrypticIBDcheck/src/IBDestp.h
CrypticIBDcheck/src/IBDest.study.c
CrypticIBDcheck/src/IBDest.sim.c
CrypticIBDcheck/NAMESPACE
CrypticIBDcheck/data
CrypticIBDcheck/data/Nhlsim.RData
CrypticIBDcheck/data/RutgersMapB36.RData
CrypticIBDcheck/R
CrypticIBDcheck/R/filters.R
CrypticIBDcheck/R/snpinfos.R
CrypticIBDcheck/R/IBDcheck.R
CrypticIBDcheck/R/IBD-class.R
CrypticIBDcheck/R/countIBS.R
CrypticIBDcheck/R/simIBD.R
CrypticIBDcheck/R/estIBD.R
CrypticIBDcheck/R/SNPgenmap.R
CrypticIBDcheck/R/cdlIBS.R
CrypticIBDcheck/R/plotIBD.R
CrypticIBDcheck/R/zzz.R
CrypticIBDcheck/vignettes
CrypticIBDcheck/vignettes/IBDcheck-hapmap.bib
CrypticIBDcheck/vignettes/CrypticIBDcheck.Rnw
CrypticIBDcheck/vignettes/fig005_all.pdf
CrypticIBDcheck/vignettes/IBDcheck-hapmap.Rnw
CrypticIBDcheck/vignettes/fig005_hs.pdf
CrypticIBDcheck/vignettes/fig005_MZ.pdf
CrypticIBDcheck/vignettes/fig005_co.pdf
CrypticIBDcheck/vignettes/fig005_fs.pdf
CrypticIBDcheck/vignettes/fig005_po.pdf
CrypticIBDcheck/MD5
CrypticIBDcheck/build
CrypticIBDcheck/build/vignette.rds
CrypticIBDcheck/DESCRIPTION
CrypticIBDcheck/man
CrypticIBDcheck/man/countIBS.Rd
CrypticIBDcheck/man/IBDcheck.Rd
CrypticIBDcheck/man/new.IBD.Rd
CrypticIBDcheck/man/plot.IBD.Rd
CrypticIBDcheck/man/filter.control.Rd
CrypticIBDcheck/man/SNPgenmap.Rd
CrypticIBDcheck/man/sim.control.Rd
CrypticIBDcheck/man/IBD.Rd
CrypticIBDcheck/man/Nhlsim.Rd
CrypticIBDcheck/man/RutgersMapB36.Rd
CrypticIBDcheck/man/CrypticIBDcheck-package.Rd