gdmp: Genomic Data Management

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Manage and analyze high-dimensional SNP data from chips with multiple densities.

Author
Gamal Abdel-Azim [aut, cre]
Date of publication
2016-09-29 23:48:56
Maintainer
Gamal Abdel-Azim <gamal.azim@gmail.com>
License
GPL (>= 2)
Version
0.1.0

View on CRAN

Man pages

arrayAppend
Append two arrays by adding new data to top array
BayesAB
Estimte SNP Effects by MCMC - Bayes (A and B) - beta
BayesCpi
Estimte SNP Effects by MCMC - Bayes C and Cpi - beta
GetHCS
Check SNP genotypes and exclude redundant SNPs
getMAF
Return frequency of the minor allele of a SNP
is.hwEq
Check a SNP for Hardy-Weinberg equilibrium
is.identical
Check two SNPs for near identity across genotyped samples
read.findhap
Read the output of Paul Vanraden's findhap,...
snpSelect
Select genotyped individuals and SNPs based on call rate,...
toArray
Turn Illumina's Genome Studio 'Final Report' file into an...

Files in this package

gdmp
gdmp/src
gdmp/src/ranlib.c
gdmp/src/gt.h
gdmp/src/com.c
gdmp/src/readGenotypes.c
gdmp/src/gt.c
gdmp/src/cIdentical.c
gdmp/src/cGetHCS.c
gdmp/src/debug.h
gdmp/src/ranlib.h
gdmp/src/cBaysCPi.c
gdmp/src/cBaysABF.c
gdmp/NAMESPACE
gdmp/R
gdmp/R/findhap.R
gdmp/R/BayesAB.R
gdmp/R/BayesCpi.R
gdmp/R/dataEdit.R
gdmp/MD5
gdmp/DESCRIPTION
gdmp/man
gdmp/man/GetHCS.Rd
gdmp/man/arrayAppend.Rd
gdmp/man/toArray.Rd
gdmp/man/snpSelect.Rd
gdmp/man/read.findhap.Rd
gdmp/man/is.hwEq.Rd
gdmp/man/getMAF.Rd
gdmp/man/BayesCpi.Rd
gdmp/man/is.identical.Rd
gdmp/man/snpRecode.rd
gdmp/man/BayesAB.Rd