% 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))

}