ecco0_ivw: Controlling for Confounding Effects in eQTL Mapping Studies...

In fanyue322/ECCO: Controlling for Confounding Effects in eQTL Mapping Studies through Joint Differential Expression and Mendelian Randomization Analyses

Description

Determining the optimal number of PEER factors for eQTL mapping analysis through DE and MR analysis

Usage

ecco0_ivw(gene, genename, gene_name, geno, ind, Y, r2 = 0.1, kb = 1)

Arguments

gene	the gene expression data.
genename	the name of the gene
gene_name	a vector containg the names of all genes
geno	a matrix containg all the cis-SNPs of the analyzed gene
ind	the index of the gene
Y	the phenotype data
r2	clumping r2 cutoff, default is 0.1
kb	clumping window, default is 1

Details

Instead of performing repetitive eQTL mapping, ECCO jointly applies differential expression analysis and Mendelian randomization (MR) analysis, leading to substantial computational savings.

Value

iv_snp

the snp that has the strongest association with the gene

Author(s)

Yue Fan, Xiang Zhou

Examples

data(exampledata)
attach(exampledata)
ind=1
genename=gene_name[ind]
gene=M_matrix[,ind]
geno=snp_raw_ivw[[ind]]
result=ecco0_ivw(gene,genename,gene_name,geno,ind,Y)
closeAllConnections()
detach(exampledata)

fanyue322/ECCO documentation built on July 11, 2020, 1:10 p.m.