--- a
+++ b/man/shaPRS_adjust.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/shaPRS.R
+\name{shaPRS_adjust}
+\alias{shaPRS_adjust}
+\title{Create lFDR corrected Q-test statistics for each SNP}
+\usage{
+shaPRS_adjust(
+  inputData,
+  rho = 0,
+  thresholds = vector(),
+  discardAmbiguousSNPs = T
+)
+}
+\arguments{
+\item{inputData}{summary statistics table that has header with the following columns: SNP    CHR    BP    Beta_A    SE_A    A1.x    A2.x    Beta_B    SE_B    A1.y    A2.y}
+
+\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{thresholds}{vector of thresholds to be used to create list of SNPs (default empty)}
+
+\item{discardAmbiguousSNPs}{(optional) if ambiguous SNPs (G/C and A/T) should be discarded (default TRUE)}
+}
+\value{
+returns object with two fields, (1) lFDRTable: a 3 column file with the following signature SNP lFDR Qval (2) hardThresholds list of SNPids that failed the heterogeneity test at each threshold
+}
+\description{
+it performs:
+(1) modified Cochran's Q-test which optionally adjusts for overlapping controls
+(2) lFDR estimation on the p-values from the above Cochran's Q-test
+(3) lists SNPs that fail the heterogeneity test at specified thresholds (optional)
+}
+\examples{
+inputDataLoc <- system.file("extdata", "shapersToydata.txt", package = "shaPRS")
+inputData= read.table(inputDataLoc, header = TRUE)
+results = shaPRS_adjust(inputData, thresholds=c(0.5,0.99))
+
+}