GWAS
swuteresa
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quantile-quantile plot (qqplot) of the p-values
The QQ plot shows the expected distribution of association test statistics (X-axis) across the million SNPs compared to the observed values (Y-axis). Any deviation from the X=Y line implies a consis转载 2013-03-11 13:10:35 · 5163 阅读 · 0 评论 -
Difference between GWAS/MAS and GS
The difference between MAS and genomic selection is that MAS only utilizes the SNPs that are significant in a GWAS, whereas genomic selection uses a genome-wide panel of dense markers so that all QTL原创 2013-03-04 14:29:46 · 1867 阅读 · 0 评论 -
数据特性概要
1.多环境2.多等位基因3.有缺失4.只有genotype和phenotype数据,没有pedigree和map(marker info)数据5.观察数(n)大于标记数(p)6.数据规模小原创 2013-04-03 11:33:32 · 701 阅读 · 0 评论 -
R Packages for GWAS and GS
rrBLUP(rrBLUPMethod6: re-parametrization of RR-BLUP to allow a fixed residual variance)BLR(功能加强BGLR,目前不支持R 3.0版本)synbreed(synbreedData)randomForestlme4:基本线性模型geneticsQTLRelGenABELsnpSt原创 2013-01-25 12:02:26 · 3339 阅读 · 2 评论 -
Breeding Value与Genotypic Value
支持和实现GWAS和GS的R Package中,只有Synbreed适合做植物育种,其他的Package都是针对动物,动物(特别是人类)数据的分析,有个重要的预处理:分析群体的HW平衡性。植物群体因为存在人为选择的问题,不可能满足HW平衡。在GWAS和GS之前,育种领域已有大量成熟的研究与应用,是基于表型分析的。育种值BV(Breeding Value),特指加性基因效应的部分。如果能原创 2013-05-12 14:08:37 · 1311 阅读 · 0 评论 -
Web sites for converting Gene IDs
http://rapdb.dna.affrc.go.jp/tools/converter原创 2014-06-02 15:31:27 · 883 阅读 · 0 评论 -
Web sites searching for Gene/Protein Names/functions
# search for Gene/Protein Names## http://grassius.org/tf_browsefamily.html?species=Rice## http://grassius.org/grasstfdb.html## http://www.shigen.nig.ac.jp/rice/oryzabase_submission/gene_no原创 2014-06-02 15:24:06 · 771 阅读 · 0 评论