Risk allele mappings

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MungeSumstats
 Type: Package
 Title: Standardise summary statistics from GWAS
-Version: 1.13.5
+Version: 1.13.6
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",

NEWS.md

@@ -1,3 +1,8 @@
+## CHANGES IN VERSION 1.13.6
+
+### New features
+* Mappings added to mapping file for risk and non risk allele.
+
 ## CHANGES IN VERSION 1.13.3
 
 ### Bug fix

R/data.R

@@ -12,11 +12,31 @@
 #' # Most the data in the below table comes from the LDSC github wiki
 #' data("sumstatsColHeaders")
 #' # Make additions to sumstatsColHeaders using github version of MungeSumstats-
+#' # Shown is an example of adding new A1 and A2 naming
+#' a1_name <- c("NON","RISK","ALLELE")
+#' a2_name <- c("RISK","ALLELE")
+#' all_delims <- c("_",".",""," ","-")
+#' all_uncorr_a1 <- vector(mode="list",length = length(all_delims))
+#' all_corr_a1 <- vector(mode="list",length = length(all_delims))
+#' all_uncorr_a2 <- vector(mode="list",length = length(all_delims))
+#' all_corr_a2 <- vector(mode="list",length = length(all_delims))
+#' for(i in seq_along(all_delims)){
+#' delim <- all_delims[i]
+#' a1 <- unlist(paste(a1_name,collapse=delim))
+#' a2 <- unlist(paste(a2_name,collapse=delim))
+#' all_uncorr_a1[[i]] <- a1
+#' all_uncorr_a2[[i]] <- a2
+#' all_corr_a1[[i]] <- "A1"
+#'   all_corr_a2[[i]] <- "A2"
+#' }
+#' se_cols <- data.frame("Uncorrected"=c(unlist(all_uncorr_a1),unlist(all_uncorr_a2)),
+#'                      "Corrected"=c(unlist(all_corr_a1),unlist(all_corr_a2)))
+#' # Or another example .....
 #' # shown is an example of adding columns for Standard Error (SE)
-#' #se_cols <- data.frame("Uncorrected"=c("SE","se","STANDARD.ERROR",
-#' #                                      "STANDARD_ERROR","STANDARD-ERROR"),
-#' #                     "Corrected"=rep("SE",5))
-#' #sumstatsColHeaders <- rbind(sumstatsColHeaders,se_cols)
+#' se_cols <- data.frame("Uncorrected"=c("SE","se","STANDARD.ERROR",
+#'                                       "STANDARD_ERROR","STANDARD-ERROR"),
+#'                      "Corrected"=rep("SE",5))
+#' sumstatsColHeaders <- rbind(sumstatsColHeaders,se_cols)
 #' #Once additions are made, order & save the new mapping dataset
 #' #now sort ordering -important for logic that 
 #' # uncorrected=corrected comes first
@@ -27,7 +47,7 @@
 #'                              sumstatsColHeaders$ordering,decreasing = TRUE),]
 #' rownames(sumstatsColHeaders)<-1:nrow(sumstatsColHeaders)
 #' sumstatsColHeaders$ordering <- NULL
-#' #manually move FRWQUENCY to above MAR - github issue 95
+#' #manually move FREQUENCY to above MAR - github issue 95
 #' frequency <- sumstatsColHeaders[sumstatsColHeaders$Uncorrected=="FREQUENCY",]
 #' maf <- sumstatsColHeaders[sumstatsColHeaders$Uncorrected=="MAF",]
 #' if(as.integer(rownames(frequency))>as.integer(rownames(maf))){