COLOC_get_res: Run coloc on GWAS-QTL object

In RajLabMSSM/catalogueR: QTL data extraction and colocalization

Run coloc on GWAS-QTL object

Description

Run coloc on GWAS-QTL object.

Usage

COLOC_get_res(
  qtl.egene,
  gwas.region,
  merge_by_rsid = TRUE,
  coloc_thresh = 0.8,
  method = "abf",
  verbose = TRUE
)

Source

library(dplyr) paths <- catalogueR::eQTLcatalogue_example_queries() query <- paths["BST1__Alasoo_2018.macrophage_IFNg"] qtl.egene <- data.frame( query )[, grep("*.QTL$|qtl_id|SNP", colnames(query), value = TRUE)] sorted_egenes <- qtl.egene |> dplyr::group_by(gene.QTL) |> dplyr::summarise(mean.P = mean(pvalue.QTL), min.P = min(pvalue.QTL)) |> dplyr::arrange(min.P) qtl.egene <- subset(qtl.egene, gene.QTL == sorted_egenes$gene.QTL[1]) gwas.region <- data.frame( query )[, grep("*.QTL$|qtl_id", colnames(query), value = TRUE, invert = TRUE)] #### Run #### coloc_res <- catalogueR:::COLOC_get_res(qtl.egene = qtl.egene, gwas.region = gwas.region)

See Also

Other coloc: COLOC_corplot(), COLOC_get_example_res(), COLOC_heatmap(), COLOC_merge_res(), COLOC_report_summary(), COLOC_run()

RajLabMSSM/catalogueR documentation built on Jan. 1, 2023, 10:45 a.m.