--- a
+++ b/man/LDRefBlend.Rd
@@ -0,0 +1,96 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/shaPRS.R
+\name{LDRefBlend}
+\alias{LDRefBlend}
+\title{Generate shaPRS specific LD reference panel}
+\usage{
+LDRefBlend(pop1LDmatrix, pop2LDmatrix, sumstatsData, memoryEfficiency = 5)
+}
+\arguments{
+\item{pop1LDmatrix}{LD reference matrix in RDS (dsCMatrix) format for target population}
+
+\item{pop2LDmatrix}{LD reference matrix in RDS (dsCMatrix) format for other population}
+
+\item{sumstatsData}{summary data with required columns of SE_A, SE_B, A1.x, A1.y, and lFDR}
+
+\item{memoryEfficiency}{larger numbers result in longer runs but lower memory usage (default 5)}
+}
+\value{
+returns a PRS specific LD matrix
+}
+\description{
+Generates a PRS specific LD reference matrix by blending together two LD ref panels according to
+shaPRS produced lFDR and standard errors
+}
+\examples{
+sumstatsData = readRDS(file = system.file("extdata", "sumstatsData_toy.rds", package = "shaPRS") )
+
+# read SNP map files (same toy data for the example)
+pop1_map_rds = readRDS(file = system.file("extdata", "my_data.rds", package = "shaPRS") )
+pop2_map_rds = readRDS(file = system.file("extdata", "my_data2.rds", package = "shaPRS") )
+
+# use chrom 21 as an example
+chromNum=21
+
+# load the two chromosomes from each population ( same toy data for the example)
+pop1LDmatrix = readRDS(file = system.file("extdata", "LDref.rds", package = "shaPRS") )
+pop2LDmatrix = readRDS(file = system.file("extdata", "LDref2.rds", package = "shaPRS") )
+
+
+# 2. grab the RSids from the map for the SNPS on this chrom,
+# each LD mat has a potentially different subset of SNPs
+# this is guaranteed to be the same order as the pop1LDmatrix
+pop1_chrom_SNPs = pop1_map_rds[ which(pop1_map_rds$chr == chromNum),]
+# this is guaranteed to be the same order as the pop2LDmatrix
+pop2_chrom_SNPs = pop2_map_rds[ which(pop2_map_rds$chr == chromNum),]
+pop1_chrom_SNPs$pop1_id = 1:nrow(pop1_chrom_SNPs)
+pop2_chrom_SNPs$pop2_id = 1:nrow(pop2_chrom_SNPs)
+
+
+# intersect the 2 SNP lists so that we only use the ones common to both LD matrices by merging them
+chrom_SNPs_df  <- merge(pop1_chrom_SNPs,pop2_chrom_SNPs, by = "rsid")
+
+# align the two LD matrices
+chrom_SNPs_df = alignStrands(chrom_SNPs_df, A1.x ="a1.x", A2.x ="a0.x", A1.y ="a1.y", A2.y ="a0.y")
+
+
+# align the summary for phe A and B
+sumstatsData = alignStrands(sumstatsData)
+
+# subset sumstats data to the same chrom
+sumstatsData = sumstatsData[which(sumstatsData$CHR == chromNum ),]
+
+# merge sumstats with common LD map data
+sumstatsData  <- merge(chrom_SNPs_df,sumstatsData, by.x="rsid", by.y = "SNP")
+
+# remove duplicates
+sumstatsData = sumstatsData[ !duplicated(sumstatsData$rsid) ,]
+# use the effect alleles for the sumstats data with the effect allele of the LD mat
+# as we are aligning the LD mats against each other, not against the summary stats
+# we only use the lFDR /SE from the sumstats,
+# which are directionless, so those dont need to be aligned
+sumstatsData$A1.x =sumstatsData$a1.x
+sumstatsData$A1.y =sumstatsData$a1.y
+
+# make sure the sumstats is ordered the same way as the LD matrix:
+sumstatsData = sumstatsData[order(sumstatsData$pop1_id), ]
+# it doesn't matter which matrix to use to order the sumstats as they are the same
+
+# subset the LD matrices to the SNPs we actually have
+pop1LDmatrix = pop1LDmatrix[sumstatsData$pop1_id,sumstatsData$pop1_id]
+pop2LDmatrix = pop2LDmatrix[sumstatsData$pop2_id,sumstatsData$pop2_id]
+
+# generate the blended LD matrix
+cormat = LDRefBlend(pop1LDmatrix,pop2LDmatrix, sumstatsData)
+
+# create a new map file that matches the SNPs common to both LD panels
+map_rds_new = pop1_map_rds[which(pop1_map_rds$chr == chromNum),]
+map_rds_new2 = map_rds_new[which(map_rds_new$rsid \%in\% sumstatsData$rsid),]
+
+# save the new LD matrix to a location of your choice
+# saveRDS(cormat,file =paste0(<YOUR LOCATION>,"/LD_chr",chromNum,".rds"))
+
+# save its Map file too
+# saveRDS(map_rds_new2,file = paste0(<YOUR LOCATION>,"/LD_chr",chromNum,"_map.rds"))
+
+}