Change function name

NAMESPACE

@@ -2,7 +2,7 @@
 
 export(calculateParamsFromCounts)
 export(calculateParamsFromIndParams)
-export(calculateVarFrac)
+export(calculateVarExp)
 export(checkInput)
 export(getGenoCorMatrix)
 export(standardizeBeta)

R/varFrac.R → 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))
     }

man/calculateParamsFromCounts.Rd

 % 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 

man/calculateParamsFromIndParams.Rd

 % 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 

man/calculateVarFrac.Rd → man/calculateVarExp.Rd

 % 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")
 
 }

man/checkInput.Rd

 % 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))

man/standardizeBeta.Rd

 % 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}