From c8b154a1678563dae04ad410216bc7bc62eb4451 Mon Sep 17 00:00:00 2001
From: Al-Murphy <alanmurph94@hotmail.com>
Date: Mon, 16 Sep 2024 11:47:41 +0100
Subject: [PATCH] Risk allele mappings

---
 DESCRIPTION                 |   2 +-
 NEWS.md                     |   5 +++++
 R/data.R                    |  30 +++++++++++++++++++++++++-----
 R/sysdata.rda               | Bin 2018 -> 2084 bytes
 data/sumstatsColHeaders.rda | Bin 2056 -> 2105 bytes
 man/sumstatsColHeaders.Rd   |  30 +++++++++++++++++++++++++-----
 6 files changed, 56 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e33a0bad..37b72a6d 100644
--- a/DESCRIPTION
+++ b/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",
diff --git a/NEWS.md b/NEWS.md
index 7d1c822f..fb1e93e6 100644
--- a/NEWS.md
+++ b/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
diff --git a/R/data.R b/R/data.R
index d23a389d..9678b139 100644
--- a/R/data.R
+++ b/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))){
diff --git a/R/sysdata.rda b/R/sysdata.rda
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diff --git a/man/sumstatsColHeaders.Rd b/man/sumstatsColHeaders.Rd
index caada99e..81ef3484 100644
--- a/man/sumstatsColHeaders.Rd
+++ b/man/sumstatsColHeaders.Rd
@@ -13,11 +13,31 @@ The code to prepare the .Rda file file from the marker file is:
 # 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
@@ -28,7 +48,7 @@ sumstatsColHeaders <-
                              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))){