diff --git a/NAMESPACE b/NAMESPACE
index 8c345364eca93f3f9cdecb36cdb1b29c522bb158..4b82019b2ad588afb33d07100ff5ba102e75a42e 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 6f9c860ae1af0f1da16dfd82cafa531df0a93368..bbc6e7ed1b1b47cc1279ea28019efddd8b38c1cd 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 3e59c894844e7afc38feead3f877c3304b6f83c7..b874863e27b8ba96ccf3753a08d3185cf7ac2707 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 2b19c949cc36a820cd5b4c3701b159017297f8a3..03e4eb5ef2a38ae542e996889a8b5c28c780d330 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 11b8aed2bbe9f6976cf773a5cf9a7f7270216d16..1506ee7058bad28ad50a08e6fdc372be8bd90609 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 55ca8823a4ac756375e8775834c818a59f510518..3e89bc4e2a3e29f931f44614ec6f324ea353f97f 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 4a85e6cc95d227a7e84fe33744d8a07fc6fa3586..de55c9266f1cbfb4a0d48439a0fbd2705b5a5098 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}