Include a call to na.omit when checking for biallelic snps

NAMESPACE

@@ -16,4 +16,5 @@ export(Zbeta_expected)
 export(Zbeta_log_rsq_over_expected)
 export(Zbeta_rsq_over_expected)
 importFrom(stats,cor)
+importFrom(stats,na.omit)
 importFrom(stats,pbeta)

R/Zalpha_BetaCDF.R

@@ -16,7 +16,7 @@
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
 #' bound of the bin.
 #'
-#' @importFrom stats cor pbeta
+#' @importFrom stats cor pbeta na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\alpha}^{BetaCDF}}{Zalpha} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -60,7 +60,7 @@ Zalpha_BetaCDF<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_Beta_a, LDp
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check dist is a numeric vector

R/Zalpha_Zscore.R

@@ -15,7 +15,7 @@
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
 #' bound of the bin.
 #'
-#' @importFrom stats cor
+#' @importFrom stats cor na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\alpha}^{Zscore}}{Zalpha} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -59,7 +59,7 @@ Zalpha_Zscore<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_rsq, LDprofi
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check dist is a numeric vector

R/Zalpha_all.R

@@ -13,7 +13,7 @@
 #' }
 #' For more information about the statistics, please see Jacobs (2016).
 #'
-#' @importFrom stats cor pbeta
+#' @importFrom stats cor pbeta na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the statistics will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -65,7 +65,7 @@ Zalpha_all <- function(pos, ws, x=NULL, dist=NULL, LDprofile_bins=NULL, LDprofil
       stop("The number of rows in x must equal the number of SNP locations given in pos")
     }
     #Check SNPs are all biallelic
-    if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+    if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
       stop("SNPs must all be biallelic")
     }
     #Change matrix x to numeric if it isn't already

R/Zalpha_log_rsq_over_expected.R

@@ -15,7 +15,7 @@
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
 #' bound of the bin.
 #'
-#' @importFrom stats cor
+#' @importFrom stats cor na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\alpha}^{log_{10}(r^2/E[r^2])}}{Zalpha} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -58,7 +58,7 @@ Zalpha_log_rsq_over_expected<-function(pos, ws, x, dist, LDprofile_bins, LDprofi
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check dist is a numeric vector

R/Zalpha_rsq_over_expected.R

@@ -15,7 +15,7 @@
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
 #' bound of the bin.
 #'
-#' @importFrom stats cor
+#' @importFrom stats cor na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\alpha}^{r^2/E[r^2]}}{Zalpha} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -58,7 +58,7 @@ Zalpha_rsq_over_expected<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_r
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check dist is a numeric vector

R/Zbeta.R

@@ -7,7 +7,7 @@
 #' \deqn{Z_{\beta}=\frac{\sum_{i \in L,j \in R}r^2_{i,j}}{|L||R|}}
 #' where \code{|L|} and \code{|R|} are the number of SNPs to the left and right of the current locus within the given window \code{ws}, and \eqn{r^2}{r^2} is equal to the squared correlation between a pair of SNPs
 #'
-#' @importFrom stats cor
+#' @importFrom stats cor na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\beta}}{Zbeta} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -44,7 +44,7 @@ Zbeta <- function(pos, ws, x, minRandL = 4, minRL = 25, X = NULL) {
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check windowsize is a number greater than 0

R/Zbeta_BetaCDF.R

@@ -16,7 +16,7 @@
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
 #' bound of the bin.
 #'
-#' @importFrom stats cor pbeta
+#' @importFrom stats cor pbeta na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\beta}^{BetaCDF}}{Zbeta} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -60,7 +60,7 @@ Zbeta_BetaCDF<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_Beta_a, LDpr
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check dist is a numeric vector

R/Zbeta_Zscore.R

@@ -15,7 +15,7 @@
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
 #' bound of the bin.
 #'
-#' @importFrom stats cor
+#' @importFrom stats cor na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\beta}^{Zscore}}{Zbeta} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -59,7 +59,7 @@ Zbeta_Zscore<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_rsq, LDprofil
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check dist is a numeric vector

R/Zbeta_log_rsq_over_expected.R

@@ -15,7 +15,7 @@
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
 #' bound of the bin.
 #'
-#' @importFrom stats cor
+#' @importFrom stats cor na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\beta}^{log_{10}(r^2/E[r^2])}}{Zbeta} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -58,7 +58,7 @@ Zbeta_log_rsq_over_expected<-function(pos, ws, x, dist, LDprofile_bins, LDprofil
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check dist is a numeric vector

R/Zbeta_rsq_over_expected.R

@@ -15,7 +15,7 @@
 #' profile should consist of evenly sized bins of distances (for example 0.0001 cM per bin), where the value given is the (inclusive) lower
 #' bound of the bin.
 #'
-#' @importFrom stats cor
+#' @importFrom stats cor na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\beta}^{r^2/E[r^2]}}{Zbeta} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -58,7 +58,7 @@ Zbeta_rsq_over_expected<-function(pos, ws, x, dist, LDprofile_bins, LDprofile_rs
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check dist is a numeric vector

R/zalpha.R

@@ -7,7 +7,7 @@
 #' \deqn{Z_{\alpha}=\frac{{|L| \choose 2}^{-1}\sum_{i,j \in L}r^2_{i,j} + {|R| \choose 2}^{-1}\sum_{i,j \in L}r^2_{i,j}}{2}}
 #' where \code{|L|} and \code{|R|} are the number of SNPs to the left and right of the current locus within the given window \code{ws}, and \eqn{r^2}{r^2} is equal to the squared correlation between a pair of SNPs
 #'
-#' @importFrom stats cor
+#' @importFrom stats cor na.omit
 #'
 #' @param pos A numeric vector of SNP locations
 #' @param ws The window size which the \eqn{Z_{\alpha}}{Zalpha} statistic will be calculated over. This should be on the same scale as the \code{pos} vector.
@@ -44,7 +44,7 @@ Zalpha <- function(pos, ws, x, minRandL = 4, minRL = 25, X = NULL) {
     stop("The number of rows in x must equal the number of SNP locations given in pos")
   }
   #Check SNPs are all biallelic
-  if(sum(apply(x,1,function(x){length(unique(x))}) != 2)>0){
+  if(sum(apply(x,1,function(x){length(na.omit(unique(x)))}) != 2)>0){
     stop("SNPs must all be biallelic")
   }
   #Check windowsize is a number greater than 0