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gdmp (version 0.2.0)

Genomic Data Management

Description

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

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Version

Install

install.packages('gdmp')

Monthly Downloads

10

Version

0.2.0

License

GPL (>= 2)

Maintainer

Gamal Abdel-Azim

Last Published

March 29th, 2019

Functions in gdmp (0.2.0)

toArray

Turn Illumina's Genome Studio ‘Final Report’ file into an array
arrayAppend

Append two arrays by adding new data to top array
BayesCpi

Estimte SNP Effects by MCMC - Bayes C and Cpi - beta
is.identical

Check two SNPs for near identity across genotyped samples
read.findhap

Read the output of Paul Vanraden's findhap, ‘genotypes.filled’
BayesAB

Estimte SNP Effects by MCMC - Bayes (A and B) - beta
GetHCS

Check SNP genotypes and exclude redundant SNPs
snpSelect

Select genotyped individuals and SNPs based on call rate, heterozygosity, HW equilibrium, or minor allele frequency.
snpRecode

Recode a matrix of SNP genotypes as 0, 1, and 2
getMAF

Return frequency of the minor allele of a SNP
is.hwEq

Check a SNP for Hardy-Weinberg equilibrium