有时候我们想画出所有SNP的LD关系图,则需要在命令行添加“-skipcheck”命令行,如下所示: java -jar Haploview.jar -skipcheck -n -pedfile 800kb1.ped -info 800kb1.info -png -out 800kb 这样就不需要经过haploview的过滤标准了. 如果只想过滤某个标准,则可参看下来参数 -skipcheck Skip all the genotype data quality checks and uses…

现在GWAS已经属于比较古老的技术了,主要是碰到严重的瓶颈了,单纯的snp与表现的关联已经不够,需要具体的生物学解释,这些snp是如何具体导致疾病的发生的. 而且,大多数病找到的都不是个别显著的snp,大多数都找到了很多的snp,而且snp都落在非编码区了,这就导致对这些snp的解读非常的困难. 目前,已经有非常傻瓜式的GWAS pipeline了,比如:A tutorial on conducting genome‐wide association studies: Quality contr…

摘要:Wright’s F‑statistics, and especially FST, provide important insights into the evolutionary processes that influence the structure of genetic variation within and among populations, and they are among the most widely used descriptive statistics in…

GWAS Catalog The NHGRI-EBI Catalog of published genome-wide association studies EBI负责维护的一个收集已发表的GWAS研究的数据库 Catalog stats Last data release on 2019-09-24 4220 publications 107486 SNPs 157336 associations Genome assembly GRCh38.p12 dbSNP Build 151 Ense…

有很多概念需要明确区分: 人有23对染色体,其中22对常染色体autosome,另外一对为性染色体sex chromosome,XX为女,XY为男. 染色体区带命名:在标示一特定的带时需要包括4项:①染色体号:②臂的符号:③区号:④在该区内的带号. 1p22表示为1号染色体短臂2区2带. 等位基因其实是一个集合,在同一个locus出现得基因型互为等位基因.Aa不能叫等位基因,正确的逻辑是:A和a是一组等位基因.由等位基因可以定义纯合和杂合. 二倍体与多倍体细胞的某些染色体上,在同一基因座上有相同…

在前几篇关于Functor和Applilcative typeclass的讨论中我们自定义了一个类型Configure,Configure类型的定义是这样的: case class Configure[+A](get: A) object Configure { implicit val configFunctor = new Functor[Configure] { def map[A,B](ca: Configure[A])(f: A => B): Configure[B] = Config…

If $p>1$, $f\geq 0$, and $$\bex F(x)=\int_0^x f(t)\rd t, \eex$$ then $$\bee\label{Hardy:0 to x} \int_0^\infty \sex{\frac{F}{x}}^p\rd x \leq \sex{\frac{p}{p-1}}^p \int_0^\infty f^p\rd x. \eee$$ Proof: $$\beex \bea \int_0^\infty \sex{\frac{F}{x}}^p\rd…

http://www.nobelprize.org/nobel_prizes/physics/laureates/1928/richardson-lecture.pdf OWEN W. RICHARDSON Thermionic phenomena and the laws which govern them Nobel Lecture, December 12, 1929 In its broadest aspect this subject may be summarized as the…

Software Development and Newton's Laws of Motion Intro I have no idea since when the word velocity found a new home in software development, it is nevertheless popular these days. However I am pretty sure that Mr. Isaac Newton would not be happy if y…

Neumann's Principle Neumann's principle, or principle of symmetry, states that, if a crystal is invariant with respect to certain symmetry elements, any of its physical properties must also be invariant with respect to the same symmetry elements, or…