From 665bbb8ce94ad9e367209740da29d3553d1a107c Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Tue, 15 Apr 2025 21:36:25 -0400
Subject: [PATCH] add documentation

---
 NAMESPACE                            |  1 +
 man/Heterogeneous_Effect.Rd          | 27 +++++++++++++++++++++++++++
 man/Ind_5traits.Rd                   |  2 +-
 man/Non_Causal_Strongest_Marginal.Rd | 27 +++++++++++++++++++++++++++
 man/Sumstat_5traits.Rd               |  5 ++---
 man/Weaker_GWAS_Effect.Rd            | 27 +++++++++++++++++++++++++++
 man/colocboost_post_inference.Rd     | 20 ++++++++++++++++++++
 7 files changed, 105 insertions(+), 4 deletions(-)
 create mode 100644 man/Heterogeneous_Effect.Rd
 create mode 100644 man/Non_Causal_Strongest_Marginal.Rd
 create mode 100644 man/Weaker_GWAS_Effect.Rd
 create mode 100644 man/colocboost_post_inference.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 46ff399..98c00be 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,7 @@
 
 export(colocboost)
 export(colocboost_plot)
+export(get_cormat)
 export(get_cos_summary)
 export(get_strong_colocalization)
 importFrom(grDevices,adjustcolor)
diff --git a/man/Heterogeneous_Effect.Rd b/man/Heterogeneous_Effect.Rd
new file mode 100644
index 0000000..99a6f6f
--- /dev/null
+++ b/man/Heterogeneous_Effect.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{Heterogeneous_Effect}
+\alias{Heterogeneous_Effect}
+\title{Summary level data for 5 traits}
+\format{
+\subsection{\code{Heterogeneous_Effect}}{
+
+A list with 3 elements
+\describe{
+\item{X}{List of genotype matrices}
+\item{Y}{List of outcomes}
+\item{TrueCausalVariants}{List of causal variants}
+}
+}
+}
+\source{
+See Cao et. al. 2025 for details. TO-DO-LIST
+}
+\usage{
+Heterogeneous_Effect
+}
+\description{
+An example dataset with simulated statistics and LD for 5 traits
+}
+\keyword{datasets}
diff --git a/man/Ind_5traits.Rd b/man/Ind_5traits.Rd
index f3b428f..6bf0c09 100644
--- a/man/Ind_5traits.Rd
+++ b/man/Ind_5traits.Rd
@@ -16,7 +16,7 @@ A list with 3 elements
 }
 }
 \source{
-FINISH
+See Cao et. al. 2025 for details. TO-DO-LIST
 }
 \usage{
 Ind_5traits
diff --git a/man/Non_Causal_Strongest_Marginal.Rd b/man/Non_Causal_Strongest_Marginal.Rd
new file mode 100644
index 0000000..147ff55
--- /dev/null
+++ b/man/Non_Causal_Strongest_Marginal.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{Non_Causal_Strongest_Marginal}
+\alias{Non_Causal_Strongest_Marginal}
+\title{Summary level data for 5 traits}
+\format{
+\subsection{\code{Non_Causal_Strongest_Marginal}}{
+
+A list with 3 elements
+\describe{
+\item{X}{List of genotype matrices}
+\item{Y}{List of outcomes}
+\item{TrueCausalVariants}{List of causal variants}
+}
+}
+}
+\source{
+See Cao et. al. 2025 for details. TO-DO-LIST
+}
+\usage{
+Non_Causal_Strongest_Marginal
+}
+\description{
+An example dataset with simulated statistics and LD for 5 traits
+}
+\keyword{datasets}
diff --git a/man/Sumstat_5traits.Rd b/man/Sumstat_5traits.Rd
index 84566f5..954fa66 100644
--- a/man/Sumstat_5traits.Rd
+++ b/man/Sumstat_5traits.Rd
@@ -7,16 +7,15 @@
 \format{
 \subsection{\code{Sumstat_5traits}}{
 
-A list with 3 elements
+A list with 2 elements
 \describe{
 \item{sumstat}{Summary statistics for 5 traits}
-\item{LD}{Matrix of LD between variants}
 \item{TrueCausalVariants}{List of causal variants}
 }
 }
 }
 \source{
-FINISH
+See Cao et. al. 2025 for details. TO-DO-LIST
 }
 \usage{
 Sumstat_5traits
diff --git a/man/Weaker_GWAS_Effect.Rd b/man/Weaker_GWAS_Effect.Rd
new file mode 100644
index 0000000..ca5b6b3
--- /dev/null
+++ b/man/Weaker_GWAS_Effect.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{Weaker_GWAS_Effect}
+\alias{Weaker_GWAS_Effect}
+\title{Summary level data for 5 traits}
+\format{
+\subsection{\code{Weaker_GWAS_Effect}}{
+
+A list with 3 elements
+\describe{
+\item{X}{List of genotype matrices}
+\item{Y}{List of outcomes}
+\item{TrueCausalVariants}{List of causal variants}
+}
+}
+}
+\source{
+See Cao et. al. 2025 for details. TO-DO-LIST
+}
+\usage{
+Weaker_GWAS_Effect
+}
+\description{
+An example dataset with simulated statistics and LD for 5 traits
+}
+\keyword{datasets}
diff --git a/man/colocboost_post_inference.Rd b/man/colocboost_post_inference.Rd
new file mode 100644
index 0000000..6703791
--- /dev/null
+++ b/man/colocboost_post_inference.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/colocboost_inference.R
+\name{get_cormat}
+\alias{get_cormat}
+\title{A fast function to calculate correlation matrix (LD matrix) from individual level data}
+\usage{
+get_cormat(X, intercepte = FALSE)
+}
+\arguments{
+\item{X}{A matrix of individual level data.}
+
+\item{intercepte}{A logical value indicating whether to include an intercept in the model. Default is FALSE.}
+}
+\value{
+A correlation matrix (LD matrix).
+}
+\description{
+This function calculates the correlation matrix (LD matrix) from individual level data.
+}
+\keyword{cb_post_inference}