--- a
+++ b/man/shaPRS_LDGen.Rd
@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/shaPRS.R
+\name{shaPRS_LDGen}
+\alias{shaPRS_LDGen}
+\title{Convenience function to generate a shaPRS specific LD reference panel for cross-ancestry analyses}
+\usage{
+shaPRS_LDGen(
+  Pop1LDRefLoc,
+  Pop2LDRefLoc,
+  blendFactorLoc,
+  adjustinputLoc,
+  outputLoc,
+  discardAmbiguousSNPs = F,
+  memoryEfficiency = 5
+)
+}
+\arguments{
+\item{Pop1LDRefLoc}{Location of the folder of the LDpred2 formatted LD-reference matrices for the 22 autosomes together with a map.rds file for the proximal study}
+
+\item{Pop2LDRefLoc}{Location of the folder of the LDpred2 formatted LD-reference matrices for the 22 autosomes together with a map.rds file for the adjunct study}
+
+\item{blendFactorLoc}{Location for the lFDR data file produced by shaPRS(), postfix: "_SNP_lFDR"}
+
+\item{adjustinputLoc}{Location for the file produced by the shaPRS(), postfix: "_adjustinput"}
+
+\item{outputLoc}{Output location}
+
+\item{discardAmbiguousSNPs}{(optional) if ambiguous SNPs (G/C and A/T) should be discarded (default TRUE)}
+
+\item{memoryEfficiency}{(optional) larger numbers result in longer runs but lower memory usage (default 5)}
+}
+\description{
+Wrapper function that loads and processes the LD data for two populations, aligns it with summary data for shaPRS and then generate a full new LD-ref panel for 22 autosomes (this should be used instead of LDRefBlend)
+}
+\examples{
+Pop1LDRefLoc <- paste0(system.file("extdata", "", package = "shaPRS"), "/")
+Pop2LDRefLoc <- paste0(system.file("extdata", "", package = "shaPRS"), "/")
+blendFactorLoc <- system.file("extdata", "pop_SNP_lFDR", package = "shaPRS")
+adjustinputLoc <- system.file("extdata", "pop_adjustinput", package = "shaPRS")
+outputLoc <- "<YOUR LOCATION>"
+# shaPRS_LDGen(Pop1LDRefLoc, Pop2LDRefLoc, blendFactorLoc, adjustinputLoc, outputLoc)
+
+}