diff --git a/inst/CITATION b/inst/CITATION index 34719dc..9cb21d5 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -6,7 +6,7 @@ citEntry( author = c(person("Xuewei", "Cao"), person("Haochen", "Sun"), person("Ru", "Feng"), - person("Rajib", "Mazumder"), + person("Rahul", "Mazumder"), person("Cristian F. B.", "Najar"), person("Yang I.", "Li"), person("Philip L.", "de Jager"), diff --git a/vignettes/LD_Free_Colocalization.Rmd b/vignettes/LD_Free_Colocalization.Rmd index aa58ee4..8a616b6 100644 --- a/vignettes/LD_Free_Colocalization.Rmd +++ b/vignettes/LD_Free_Colocalization.Rmd @@ -129,13 +129,22 @@ for (i in 1:length(X)){ x <- X[[i]] y <- Y[[i]] effect_n[i] <- length(y) - rr <- susieR::univariate_regression(X = x, y = y) - effect_est <- cbind(effect_est, rr$betahat) - effect_se <- cbind(effect_se, rr$sebetahat) + # simply use `rr <- susieR::univariate_regression(X = x, y = y)` + output = matrix(0,ncol(x),2) + for (i in 1:ncol(x)) { + fit = summary(lm(y ~ x[,i]))$coef + if (nrow(fit) == 2) + output[i,] = as.vector(fit[2,1:2]) + else + output[i,] = c(0,0) + } + effect_est <- cbind(effect_est, output[,1]) + effect_se <- cbind(effect_se, output[,2]) } colnames(effect_est) <- colnames(effect_se) <- c("Y1", "Y2", "Y3", "Y4", "Y5") rownames(effect_est) <- rownames(effect_se) <- colnames(X[[1]]) + # Run colocboost res <- colocboost(effect_est = effect_est, effect_se = effect_se, effect_n = effect_n) diff --git a/vignettes/Summary_Statistics_Colocalization.Rmd b/vignettes/Summary_Statistics_Colocalization.Rmd index 17dcaba..1ddd97e 100644 --- a/vignettes/Summary_Statistics_Colocalization.Rmd +++ b/vignettes/Summary_Statistics_Colocalization.Rmd @@ -189,9 +189,17 @@ for (i in 1:length(X)){ x <- X[[i]] y <- Y[[i]] effect_n[i] <- length(y) - rr <- susieR::univariate_regression(X = x, y = y) - effect_est <- cbind(effect_est, rr$betahat) - effect_se <- cbind(effect_se, rr$sebetahat) + # simply use `rr <- susieR::univariate_regression(X = x, y = y)` + output = matrix(0,ncol(x),2) + for (i in 1:ncol(x)) { + fit = summary(lm(y ~ x[,i]))$coef + if (nrow(fit) == 2) + output[i,] = as.vector(fit[2,1:2]) + else + output[i,] = c(0,0) + } + effect_est <- cbind(effect_est, output[,1]) + effect_se <- cbind(effect_se, output[,2]) } colnames(effect_est) <- colnames(effect_se) <- c("Y1", "Y2", "Y3", "Y4", "Y5") rownames(effect_est) <- rownames(effect_se) <- colnames(X[[1]])