--- a
+++ b/man/GPROB.Rd
@@ -0,0 +1,72 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gprob.R
+\name{GPROB}
+\alias{GPROB}
+\title{GPROB}
+\usage{
+GPROB(prevalence, or, geno)
+}
+\arguments{
+\item{prevalence}{A numeric vector with prevalence of each phenotype in the population.}
+
+\item{or}{A matrix with odds ratios for each phenotype (column) and genetic variant (row).}
+
+\item{geno}{A matrix with risk allele counts for each person (row) and genetic variant (column).}
+}
+\value{
+A list with the population-level probabilities for each person to
+have each phenotype, and the conditional probabilities, assuming that each
+person has one of the phenotypes.
+}
+\description{
+Many diseases may have similar presentations in the clinic. By
+using genetic information, it may sometimes be possible to prioritize some
+diagnoses over others. GPROB implements calculations of genetic probability
+from genotypes and effect sizes for genetic variants associated with
+diseases.
+}
+\examples{
+prevalence <- c("RA" = 0.001, "SLE" = 0.001)
+or <- read.delim(
+  sep = "",
+  row.names = 1,
+  text = "
+snp  RA SLE
+SNP1 1.0 0.4
+SNP2 1.0 0.9
+SNP3 1.0 1.3
+SNP4 0.4 1.6
+SNP5 0.9 1.0
+SNP6 1.3 1.0
+SNP7 1.6 1.0
+")
+or <- as.matrix(or)
+geno <- read.delim(
+  sep = "",
+  row.names = 1,
+  text = "
+id SNP1 SNP2 SNP3 SNP4 SNP5 SNP6
+ 1    0    1    0    2    1    0
+ 2    0    0    1    0    2    2
+ 3    1    0    1    1    0    2
+ 4    1    1    0    2    0    0
+ 5    0    1    1    1    1    0
+ 6    0    0    1    3    0    2
+ 7    2    2    2    2    2    2
+ 8    1    2    0    2    1    1
+ 9    0    2    1   NA    1    2
+10    1    0    2    2    2    0
+")
+geno <- as.matrix(geno)
+ix <- apply(geno, 1, function(x) !any(is.na(x)))
+geno <- geno[ix,]
+ix <- apply(geno, 1, function(x) !any(x < 0 | x > 2))
+geno <- geno[ix,]
+or <- or[colnames(geno),]
+GPROB(prevalence, or, geno)
+}
+\references{
+{
+\insertRef{Knevel2020}{GPROB}
+}
+}