MaizeSNPDB

A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines. This R script chara-2-sparse.R is used to convert a traditional character genotype matrix into an integer sparse genotype matrix. This R script can be used in the system command line with R installed in the system or be used in the R enviroment. test.snp.RData is the input data to this R script. test.snp.RData is an R data file contained the genotype data of 1210 maize lines across 1000 SNP sites in character matrix. The content of this R data can be viewed in the R enviroment as shown below. MaizeSNPDB is deployed at http://150.109.59.144:3838/MaizeSNPDB/ for online use. The genotypes of 1210 maize lines at 35,370,939 SNP sites are stored using Sparse Matrices in R. MaizeSNPDB is idle until you activate it by accessing the URL. After running the R script, a new R data file named as test.snp. Mat.

Webpage:
https://github.com/venyao/MaizeSNPDB

Publications:

Tags:

dna polymorphism genotype and phenotype data management phylogenetics

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