--- a
+++ b/man/shaPRS.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/shaPRS.R
+\name{shaPRS}
+\alias{shaPRS}
+\title{Creates a new set of summary statistics}
+\usage{
+shaPRS(
+  proximalLoc,
+  adjunctLoc,
+  outputLoc,
+  rho = 0,
+  discardAmbiguousSNPs = T,
+  useProximalForMissing = T
+)
+}
+\arguments{
+\item{proximalLoc}{proximal LDPred formatted GWAS summary statistics table  that has header with the following columns: chr    pos    SNP    A1    A2    Freq1.Hapmap    b    se    p    N}
+
+\item{adjunctLoc}{dataframe for adjunct dataset of the same signature}
+
+\item{outputLoc}{the location of the output files}
+
+\item{rho}{estimate of correlation between studies due to shared subjects. 0 for no overlap and 1 for complete overlap. default: 0. Obtain this from shaPRS_rho()}
+
+\item{discardAmbiguousSNPs}{(optional) if ambiguous SNPs (G/C and A/T) should be discarded (default TRUE)}
+
+\item{useProximalForMissing}{(optional) if SNPs missing from the adjunct data should be kept using the proximal data or not (default TRUE)}
+}
+\description{
+it performs both steps of the shaPRS method in a single call:
+(1) Creates lFDR corrected Q-test statistics for each SNP (via shaPRS_adjust)
+(2) produce summary statistics according to a continuous weighting scheme (via shaPRS_blend_overlap)
+(3) It writes to disk the following files with postfixes:   "_adjustinput", "_SNP_lFDR", "_shaprs", "_meta", which are the input and output for shaPRS_adjust (also required for shaPRS_LDGen), and shaPRS adjusted summary stats and a fixed-effect meta-analysis
+}
+\examples{
+proximalLoc <- system.file("extdata", "phenoA_sumstats", package = "shaPRS")
+adjunctLoc <- system.file("extdata", "phenoB_sumstats", package = "shaPRS")
+shaPRS(proximalLoc, adjunctLoc, tempfile())
+
+}