GTEx.PrCa: Real data for selecting the genes on chromosome 10 for the...

In USCbiostats/hJAM: Hierarchical Joint Analysis of Marginal Summary Statistics

Real data for selecting the genes on chromosome 10 for the risk of prostate cancer

Description

Real data for selecting the genes on chromosome 10 for the risk of prostate cancer

Format

The GTEx.PrCa is a set of data sets which was applied for selecting the genes on chromosome 10 for the risk of prostate cancer

GTEx.PrCa.IVWmarginal.A

The marginal \hat{A} matrix with 158 genes and 182 eQTLs. The raw data was downloaded from GTEx analysis v7 (https://gtexportal.org/home/datasets). Priority Pruner was used to select the independent eQTLs. We used this matrix for MR-BMA implementation.)

GTEx.PrCa.marginal.A

The marginal \hat{A} matrix with 167 genes and 447 eQTLs. The raw data was downloaded from GTEx analysis v7 (https://gtexportal.org/home/datasets). This is the raw \hat{A} matrix for constructing the conditional weight matrix for SHA-JAM analysis.

GTEx.PrCa.marginal.A.se

The standard errors of the marginal \hat{A} effects for the SNP-gene pairs (167 genes, 447 eQTLs). The raw data was downloaded from GTEx analysis v7 (https://gtexportal.org/home/datasets).

GTEx.PrCa.inclusion.indicator

The inclusion indicator for the significant SNP-gene pairs (167 genes, 447 eQTLs). Significant as 1; otherwise 0. This matrix is for composing the conditional weight matrix using the raw data.

GTEx.PrCa.Amatrix

The conditional \hat{A} matrix with 167 genes and 447 eQTLs, which was composed by SuSiE JAM and the raw data of \hat{A} matrix.

GTEx.PrCa.Geno

The reference genotype data for the 447 eQTLs from the European-ancestry population in 1000 Genome Project (Consortium, 2015)

GTEx.PrCa.betas.gwas

The b vector. The association estimates between eQTLs and the risk of prostate cancer from (Schumacher et al., 2018)

GTEx.PrCa.betas.se.gwas

The se(b) vector from (Schumacher et al., 2018)

GTEx.PrCa.pvalue.gwas

The pvalues vector of the association estimates between selected SNPs and the risk of prostate cancer from (Schumacher et al., 2018)

GTEx.PrCa.maf.gwas

The vector of the effect allele frequency of the SNPs from (Schumacher et al., 2018)

References

Consortium GP. A global reference for human genetic variation. Nature 2015; 526: 68.

Lonsdale, John, et al. The genotype-tissue expression (GTEx) project. Nature genetics 45.6 (2013): 580-585.

Schumacher, Fredrick R., et al. Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci. Nature genetics 50.7 (2018): 928-936.

USCbiostats/hJAM documentation built on Jan. 26, 2024, 5:27 p.m.