Although the genome-wide significance P-value threshold of 5 脳 10(-8) has become a standard for common-variant GWAS, it has not been updated to cope with the lower allele frequency spectrum used in many recent array-based GWAS studies and sequencing studies. Using a whole-genome- and -...
for(i in p.threshold){ # Go through each p-value threshold prs <- read.table(paste0("EUR.",i,".profile"), header=T) # Merge the prs with the phenotype matrix # We only want the FID, IID and PRS from the PRS file, therefore we only select the ...
A 5% FDR-adjusted P-value threshold of P < 0.0244 was calculated using the Benjamini-Hochberg165 method, yielding 55/108 significant tests, and 20/30 significant SNP replications in at least one cranial vault segment. FST enrichment analysis...
--geno, and/or applying different p-value thresholds to distinct subsets of your data. --hwe: 2 variants removed due to Hardy-Weinberg exact test. 344283 variants removed due to minor allele threshold(s) (--maf/--max-maf/--mac/--max-mac). 1113612 variants and 165 people pass filters ...
(--geno).Warning:--hwe observation counts vary by more than10%.Consider using--geno,and/or applying different p-value thresholds to distinct subsetsofyour data.--hwe:2variants removed due to Hardy-Weinberg exact test.344283variants removed due to minor allelethreshold(s)(--maf/--max-maf/-...
选择HWE p-value低于0.00001的SNP绘图,以放大严重偏离的SNP awk'{ if ($9 <0.00001) print $0 }'plink.hwe>plinkzoomhwe.hwe Rscript --no-save hwe.R [外链图片转存失败,源站可能有防盗链机制,建议将图片保存下来直接上传(img-EFz5VZ4L-1596263025964)(https://upload-images.jianshu.io/upload_images/...
曼哈顿图:在生物和统计学上,做频率统计、突变分布、GWAS关联分析的时候,我们经常会看到一些非常漂亮的manhattan plot,能够对候选位点的分布和数值一目了然。位点坐标和pvalue。map文件至少包含三列——染色体号,SNP名字,SNP物理位置。assoc文件包含SNP名字和pvalue。haploview即可画出。
检查时,排除了这些SNP,并使用参数--indep-pairwise来精简SNP。参数参数“ 50 5 0.2”分别代表:窗口大小,每步移动窗口经过的SNP数量(步长),以及一个SNP在所有其他SNP上同时回归的多重相关系数(multiple correlation coefficient for a SNP being regressed on all other SNPs simultaneously)(即r^2 threshold)。
#Load the saved file and filter according to aP-value threshold GWAS_QTL_merge_subset<-subset(GWAS_QTL_merge,Pval<pvalue_cutoff)save(GWAS_QTL_merge_subset,file="../tmp_data/GWAS_QTL_merge_subset.Rdata") 转换RSID 代码语言:javascript ...
曼哈顿图：在⽣物和统计学上，做频率统计、突变分布、GWAS关联分析的时候，我们经常会看到⼀些⾮常漂亮的manhattan plot，能够对候选位点的分布和数值⼀⽬了然。位点坐标和pvalue。map⽂件⾄少包含三列——染⾊体号，SNP名字，SNP物理位置。assoc⽂件包含SNP名字和pvalue。haploview即可画出。SNP的本质...