% 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}
}
}