diff --git a/DESCRIPTION b/DESCRIPTION index 686d315..e108f88 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: colocboost Type: Package Date: 2025-04-22 Title: Multi-Context Colocalization Analysis for QTL and GWAS Studies -Version: 0.5.0 +Version: 1.0.0 Authors@R: c( person(given = "Xuewei", family = "Cao", email = "xc2270@cumc.columbia.edu", role = c("cre", "aut", "cph")), person(given = "Haochen", family = "Sun", email = "hs3393@cumc.columbia.edu", role = c("aut", "cph")), diff --git a/R/data.R b/R/data.R index 32950da..eb49650 100644 --- a/R/data.R +++ b/R/data.R @@ -100,8 +100,9 @@ #' @format ## `Ambiguous_Colocalization` #' A list with 2 elements #' \describe{ -#' \item{ColocBoost_Results}{A `colocboost` output objective} -#' \item{SuSiE_Results}{Two `susie` output objective for eQTL and GWAS} +#' \item{ColocBoost_Results}{A `colocboost` output object} +#' \item{SuSiE_Results}{Two `susie` output object for eQTL and GWAS} +#' \item{COLOC_V5_Results}{A `coloc` output object} #' } #' @source The Ambiguous_Colocalization dataset contains a real data example from one of our real data applications, #' which shows an ambiguous colocalization between eQTL and GWAS. diff --git a/data/Ambiguous_Colocalization.rda b/data/Ambiguous_Colocalization.rda index b36f259..7a5f254 100644 Binary files a/data/Ambiguous_Colocalization.rda and b/data/Ambiguous_Colocalization.rda differ diff --git a/man/Ambiguous_Colocalization.Rd b/man/Ambiguous_Colocalization.Rd index 28dbccc..0cb0012 100644 --- a/man/Ambiguous_Colocalization.Rd +++ b/man/Ambiguous_Colocalization.Rd @@ -9,8 +9,9 @@ A list with 2 elements \describe{ -\item{ColocBoost_Results}{A \code{colocboost} output objective} -\item{SuSiE_Results}{Two \code{susie} output objective for eQTL and GWAS} +\item{ColocBoost_Results}{A \code{colocboost} output object} +\item{SuSiE_Results}{Two \code{susie} output object for eQTL and GWAS} +\item{COLOC_V5_Results}{A \code{coloc} output object} } } } diff --git a/vignettes/Ambiguous_Colocalization.Rmd b/vignettes/Ambiguous_Colocalization.Rmd index a93faed..2bebfa3 100644 --- a/vignettes/Ambiguous_Colocalization.Rmd +++ b/vignettes/Ambiguous_Colocalization.Rmd @@ -39,6 +39,8 @@ This dataset is structured as a list with two main components: 2. `SuSiE_Results`: Contains fine-mapping results from the SuSiE algorithm for both eQTL and GWAS data separately. +3. `COLOC_V5_Results`: Contains colocalization results from COLOC, which is directly from two `susie` output objects. + # 2. ColocBoost results @@ -111,6 +113,26 @@ susieR::susie_plot(susie_eQTL, y = "PIP", pos = 2000:n_variables) susieR::susie_plot(susie_GWAS, y = "PIP", pos = 2000:n_variables) ``` + + +We also show the colocalization results from COLOC method. For this ambiguous colocalization, COLOC shows + +- A high posterior probability of colocalization (PP.H4) of 0.85. +- Two hits are corresponding to variants with highest PIP in SuSiE for eQTL and GWAS, separately. + +Note that SuSiE-based COLOC has a relatively high confidence of this as a colocalization event because each of SuSiE 95% CS as shown above cover substantially larger region +(containing more variants) compared to the trait-specific effects identified by ColocBoost, although at a lower purity (SuSiE purity = 0.56 and 0.64, ColocBoost uCoS purity = 0.67 and 0.70). +With larger overlap between the SuSiE 95% CS across traits, the high probability of colocalization is expected. But for this particular data application without knowing the ground truth, +it is difficult to determine which method is more precise. + +```{r coloc-results} +# To run COLOC, please use the following command: +# res <- coloc::coloc.susie(susie_eQTL, susie_GWAS) +res <- Ambiguous_Colocalization$COLOC_V5_Results +res$summary +``` + + # 3. Get the ambiguous colocalization results and summary ColocBoost provides a function to get the ambiguous colocalization results and summary from trait-specifc effects, by considering the correlation of variants between the two uCoS.