From ccb681fa76bf033ffa6522409730a4793959e130 Mon Sep 17 00:00:00 2001
From: Vincent LAVILLE <vincent.laville@pasteur.fr>
Date: Tue, 21 Nov 2017 12:23:45 +0100
Subject: [PATCH] Change function name
---
NAMESPACE | 2 +-
R/{varFrac.R => varExp.R} | 8 ++++----
man/calculateParamsFromCounts.Rd | 2 +-
man/calculateParamsFromIndParams.Rd | 2 +-
man/{calculateVarFrac.Rd => calculateVarExp.Rd} | 14 +++++++-------
man/checkInput.Rd | 8 +++++---
man/standardizeBeta.Rd | 2 +-
7 files changed, 20 insertions(+), 18 deletions(-)
rename R/{varFrac.R => varExp.R} (95%)
rename man/{calculateVarFrac.Rd => calculateVarExp.Rd} (77%)
diff --git a/NAMESPACE b/NAMESPACE
index 8c34536..4b82019 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,7 +2,7 @@
export(calculateParamsFromCounts)
export(calculateParamsFromIndParams)
-export(calculateVarFrac)
+export(calculateVarExp)
export(checkInput)
export(getGenoCorMatrix)
export(standardizeBeta)
diff --git a/R/varFrac.R b/R/varExp.R
similarity index 95%
rename from R/varFrac.R
rename to R/varExp.R
index 6f9c860..bbc6e7e 100644
--- a/R/varFrac.R
+++ b/R/varExp.R
@@ -144,15 +144,15 @@ standardizeBeta <- function(betaG,betaINT,maf,meanE,varE,type) {
#' matcor <- cor(matrix(runif(5*5, 1, 5), nrow = 5))
#' varY <- 2.25
#' N <- 100000
-#' calculateVarFrac(std_bG, std_bI, matcor, varY, N, "G")
-#' calculateVarFrac(std_bG, std_bI, matcor, varY, N, "I")
-#' calculateVarFrac(std_bG, std_bI, matcor, varY, N, "J")
+#' calculateVarExp(std_bG, std_bI, matcor, varY, N, "G")
+#' calculateVarExp(std_bG, std_bI, matcor, varY, N, "I")
+#' calculateVarExp(std_bG, std_bI, matcor, varY, N, "J")
#'
#' @importFrom MASS ginv
#'
#' @export
#'
-calculateVarFrac <- function(std_bG, std_bI, matcor, varY, N, type) {
+calculateVarExp <- function(std_bG, std_bI, matcor, varY, N, type) {
if (type == "G") {
std_bI <- rep(0, length(std_bG))
}
diff --git a/man/calculateParamsFromCounts.Rd b/man/calculateParamsFromCounts.Rd
index 3e59c89..b874863 100644
--- a/man/calculateParamsFromCounts.Rd
+++ b/man/calculateParamsFromCounts.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/varFrac.R
+% Please edit documentation in R/varExp.R
\name{calculateParamsFromCounts}
\alias{calculateParamsFromCounts}
\title{Calculate the mean and variance of a binary variable in a pooled sample
diff --git a/man/calculateParamsFromIndParams.Rd b/man/calculateParamsFromIndParams.Rd
index 2b19c94..03e4eb5 100644
--- a/man/calculateParamsFromIndParams.Rd
+++ b/man/calculateParamsFromIndParams.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/varFrac.R
+% Please edit documentation in R/varExp.R
\name{calculateParamsFromIndParams}
\alias{calculateParamsFromIndParams}
\title{Calculate the mean and variance of a quantitative variable in a pooled sample
diff --git a/man/calculateVarFrac.Rd b/man/calculateVarExp.Rd
similarity index 77%
rename from man/calculateVarFrac.Rd
rename to man/calculateVarExp.Rd
index 11b8aed..1506ee7 100644
--- a/man/calculateVarFrac.Rd
+++ b/man/calculateVarExp.Rd
@@ -1,11 +1,11 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/varFrac.R
-\name{calculateVarFrac}
-\alias{calculateVarFrac}
+% Please edit documentation in R/varExp.R
+\name{calculateVarExp}
+\alias{calculateVarExp}
\title{Calculate the fraction of phenotypic variance explained by as set of
significant genetic effect and/or interaction effects.}
\usage{
-calculateVarFrac(std_bG, std_bI, matcor, varY, N, type)
+calculateVarExp(std_bG, std_bI, matcor, varY, N, type)
}
\arguments{
\item{std_bG}{is the vector of standardized genetic effect sizes}
@@ -37,8 +37,8 @@ std_bI <- rnorm(5, 0, 0.001)
matcor <- cor(matrix(runif(5*5, 1, 5), nrow = 5))
varY <- 2.25
N <- 100000
-calculateVarFrac(std_bG, std_bI, matcor, varY, N, "G")
-calculateVarFrac(std_bG, std_bI, matcor, varY, N, "I")
-calculateVarFrac(std_bG, std_bI, matcor, varY, N, "J")
+calculateVarExp(std_bG, std_bI, matcor, varY, N, "G")
+calculateVarExp(std_bG, std_bI, matcor, varY, N, "I")
+calculateVarExp(std_bG, std_bI, matcor, varY, N, "J")
}
diff --git a/man/checkInput.Rd b/man/checkInput.Rd
index 55ca882..3e89bc4 100644
--- a/man/checkInput.Rd
+++ b/man/checkInput.Rd
@@ -1,8 +1,9 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/varFrac.R
+% Please edit documentation in R/varExp.R
\name{checkInput}
\alias{checkInput}
-\title{Make sure}
+\title{Make sure SNPs in the input file and SNPs included
+in the correlation matrix are the same.}
\usage{
checkInput(df, v)
}
@@ -15,7 +16,8 @@ checkInput(df, v)
A data frame only with rows corresponding to SNPs in the vector \code{v}
}
\description{
-Make sure
+This step is necessary because some SNPs in the input may be not
+found in the reference panel or excluded from the matrix after the pruning step.
}
\examples{
df <- data.frame(c("rs1", "rs2", "rs3"), rnorm(3))
diff --git a/man/standardizeBeta.Rd b/man/standardizeBeta.Rd
index 4a85e6c..de55c92 100644
--- a/man/standardizeBeta.Rd
+++ b/man/standardizeBeta.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/varFrac.R
+% Please edit documentation in R/varExp.R
\name{standardizeBeta}
\alias{standardizeBeta}
\title{Derive betas in the standardized model from betas in the general model}
--
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