9 Matching Annotations
  1. Jul 2021
    1. 实际上,将黄元吉丹道思想归入中派更重要的理由即是他的“玄关”理论,黄元吉全部丹诀即以“玄关一窍”为轴心。在虚寂杳冥的玄关态,非阴非阳,即阴即阳,非虚非实,即虚即实,这样的中道零点位正是诸子百家共同奉守之圭臬。此外,黄元吉在《乐育堂语录》中指陈了千古丹经所未发的日用伦常之间的阳生活子时,这种居尘出尘,身在尘世而不被尘世所蔽,不离现实生活而超越现实生活,举凡无不恰到好处、随心所欲而无不中规中矩,在行住坐卧之间无处不阳生、无时不阳生,此岸即是彼岸。这样的丹道阳生观正折射了中国文化的核心精神气质,依时而中,依中而行。阳生活子时本来是丹道景象,黄元吉将阳生与“孔颜之乐”、贞女烈士之舍生取义、私欲褪尽之灵光独耀融会贯通,这一思想颠覆了认为只有深山静坐才能触发阳生的狭隘丹道观念,其意义在丹道史上、乃至中国思想史上皆是非凡的。

      秒啊!秒!

  2. May 2021
    1. For example, performing downstream analyses with only 5 PCs does significantly and adversely affect results

      这个要注意,居然不能只用5个PC

  3. Apr 2021
    1. This protocol uses a window of 1500 variants, shifted by 10% for each new round of comparisons, and a threshold of R 2  > 0.2. The window size of 1500 variants corresponds to the large, high LD chromosome 8 inversion, while the shift of 10% represents a trade-off between efficiency and thoroughness

      测试过,pure LD后没有关联位点了。可能是假阳性?

    2. It is necessary to remove rare variants from GWAS because the certainty of the genotype call is reduced by their low minor allele count. Even in common variants, however, genotyping and genotype recalling are subject to technical error, with the result that a proportion of variants and samples are of low quality, and should be removed from the analysis.

      稀有变异的检出率不是很可靠?

    3. For the smallest studies, where fewer than 1000 individuals are investigated, a cut-off of 5% should be considered—this is in line with the analysis program GenAbel, for example, which uses a minor allele count of 5 as its cut-off [ 18 ].

      1000个样本以下推荐5%的maf,有空要测试一下

  4. Mar 2021
    1. The expectation is that IBD = 1 for duplicates or monozygotic twins, IBD = 0.5 for first-degree relatives, IBD = 0.25 for second-degree relatives and IBD = 0.125 for third-degree relatives. Due to genotyping error, LD and population structure there is often some variation around these theoretical values and it is typical to remove one individual from each pair with an IBD > 0.1875, which is halfway between the expected IBD for third- and second-degree relatives. For these same reasons an IBD > 0.98 identifies duplicates.

      IBD过滤标准.IBD即plink结果中的PI_HAT。

    2. The method works best when only independent SNPs are included in the analysis. To achieve this, regions of extended linkage disequilibrium (LD) (such as the HLA) are entirely removed from the dataset8 and remaining regions are typically pruned so that no pair of SNPs within a given window (say, 50kb) is correlated (typically taken as r2>0.2)

      LD过滤,但实际发现过滤后位点很少,关联效应很弱

    1. Our primary aim was to generate a cohort large enough to examine the heritability of prognostic therapy outcomes. However, the meta-analysis estimate of SNP heritability was low and non-significant (h2SNP = 0.09, SE = 0.17). A sample size of 2724 has 80% and 99% power to detect a SNP-heritability of 33% and 50%, respectively94. To achieve 80% power to detect a heritability of 20%, a sample of 4500 individuals will be required. A meta-analysis of 2 799 individuals was sufficient to detect a significant heritability estimate for therapy outcome to antidepressant drugs (h2SNP = 0.42, SE = 0.18) and this was the first evidence of a genetic component for treatments outcome of any kind

      统计方法值得学习

    2. The meta-analysis sample (n = 2724) had 80% power to detect variants explaining 1.5% of the variance and 42% power to detect variants explaining 1% of the variance. Therefore, it is not especially surprising that we do not detect any variants at genome-wide significance. Typically, GWAS of psychological traits have required tens of thousands of participants to detect SNPs at genome-wide significance

      心理疾病GWAS研究艰难,2724个样本的meta分析结果还是阴性