if(!requireNamespace("remotes",quietly=TRUE))install.packages("remotes")if(!requireNamespace("MRInstruments",quietly=TRUE))remotes::install_github("MRCIEU/MRInstruments")library(MRInstruments) 2.GWAS catalog: data(gwas_catalog)head(gwas_catalog)#例如,使用Speliotes等人2010年的研究获得BMI的工具变量...
步骤1、我们可以在GWAS Catalog中按论文的PMID(33414549)进行搜索: 步骤2、下拉至Studies,点击非认知能力表型相应的编号:GCST90011874: 步骤3、找到Full Summary Statistics,这里代表的就是能够获得完整GWAS Summary Results的地方(again,凡事没有绝对,不一定每一个表型都提供): 步骤4、下载GWAS Summary Results至本地...
head(f) write.table(f,"GWAS_AF_Finn.txt",sep = "\t",row.names = FALSE,quote = FALSE) #SMR/GSMR格式转化---GWAS catalog格式 library(tidyverse) library(data.table) setwd("稳健分析GCST274790_AF6414andFinn/GSMR/") g<-fread("AF-GCST006414-build37.f.tsv.gz") #读取GWAS数据 head(g)...
GWAS Catalog:https://www.ebi.ac.uk/gwas/ GWAS Central:https://www.gwascentral.org/ Case Control GWAS (Genome Wide Association Study) Database:https://gwas.biosciencedbc.jp/cgi-bin/gwasdb/gwas_top.cgi GWAS atlas:https://atlas.ctglab.nl/ UKBB GWAS:https://www.ukbiobank.ac.uk/tag/gwas...
We carried out a meta-analysis using data from the NHGRI-EBI GWAS Catalog in order to explore the observed distribution of locus effects for a set of 42 complex traits and to quantify their contribution to narrow-sense heritability. With the data at hand, we were able to predict the ...
GWAS Catalogview FAIRsharing entry Metabolomics & Proteomics We ask authors to submit proteomics data to members of theProteomeXchangeconsortium (listed below), following theMIAPE recommendations. MassIVEview FAIRsharing entry MetaboLightsview FAIRsharing entry ...
分析方法: 使用MANOVA对寿命、健康寿命、父母寿命三个不同的GWAS summary文件进行荟萃分析。随后对感兴趣的基因座按照性别和年龄进行分层分析,用GWAS catalog和PhenoScanner查找感兴趣基因的相关表型。使用SMR进行基因表达共定位分析,使用FUMA的Gene2Func进行基因富集分析,使用TwoSampleMR进行孟德尔随机化随机化; ...
九、GWAS wgethttp://www.genome.gov/admin/gwascatalog.txt 十、snp147.txt.gz(该网站包含了Annotation database) wgethttp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp147.txt.gz hg38:http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ ...
Jian Yang and colleagues propose a method that integrates summary data from GWAS and eQTL studies to identify genes whose expression levels are associated with complex traits because of pleiotropy. They apply the method to five human complex traits and p
Methods: MR-Base and LD Hub are built on a database of harmonized summary genetic data from GWAS consortia, dbGAP and the GWAS catalog, roughly corresponding to >1,200,000 individuals and approximately 2000 phenotypes. Queries to both are submitted through platform-specific web portals. LD Hub...