From c55aaa79a9fd926c0473e7243ec6f96e68c3d888 Mon Sep 17 00:00:00 2001
From: Al-Murphy <alanmurph94@hotmail.com>
Date: Fri, 8 Dec 2023 15:27:32 +0000
Subject: [PATCH] update check ldsc n comp

---
 DESCRIPTION           |  2 +-
 NEWS.md               |  6 ++++++
 R/check_ldsc_format.R | 32 ++++++++++++++++++++-----------
 R/sort_coords.R       | 44 +++++++++++++++++++++----------------------
 man/sort_coords.Rd    |  3 ---
 5 files changed, 49 insertions(+), 38 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 42ba912..40e8751 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MungeSumstats
 Type: Package
 Title: Standardise summary statistics from GWAS
-Version: 1.11.1
+Version: 1.11.2
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",
diff --git a/NEWS.md b/NEWS.md
index 2ed4de5..c13f8cf 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+## CHANGES IN VERSION 1.11.2
+
+### Bug fix
+* Remove unused argument `make_ordered` from `sort_coords()`
+* Issue fixed with check ldsc format wehn compute_n type chosen 
+
 ## CHANGES IN VERSION 1.11.1
 
 ### Bug fix
diff --git a/R/check_ldsc_format.R b/R/check_ldsc_format.R
index 58c7e5a..335e3f9 100644
--- a/R/check_ldsc_format.R
+++ b/R/check_ldsc_format.R
@@ -34,20 +34,30 @@ check_ldsc_format <- function(sumstats_dt, save_format, convert_n_int,
             message()
             allele_flip_check <- TRUE
         }
-        if (!compute_z && !z_present) {
-            message("Setting `compute_z=TRUE` to comply with LDSC format.")
-            compute_z <- TRUE
-        }
         n_msg <- paste0(
-            "LDSC requires an N column but your dataset doesn't ",
-            "appear to have one. You can impute an N value for ",
-            "all your SNPs\nby setting `compute_n` to this value but",
-            " note this is may not be correct and may lead to ",
-            "different results from LDSC\nthan if the true N per SNP",
-            " was known."
+          "LDSC requires an N column but your dataset doesn't ",
+          "appear to have one. You can impute an N value for ",
+          "all your SNPs\nby setting `compute_n` to this value but",
+          " note this is may not be correct and may lead to ",
+          "different results from LDSC\nthan if the true N per SNP",
+          " was known."
         )
+        if (!z_present && isFALSE(compute_z)) {
+          beta_se_present <- ("BETA" %in% names(sumstats_dt) && 
+                                "SE" %in% names(sumstats_dt))
+          p_present <- "P" %in% names(sumstats_dt)
+          if(beta_se_present){
+            message("Setting `compute_z=BETA` to comply with LDSC format.")
+            compute_z <- "BETA"
+          }else if(p_present){
+            message("Setting `compute_z=P` to comply with LDSC format.")
+            compute_z <- "P"
+          } else{
+            stop(n_msg)  
+          } 
+        }
         if (compute_n == 0L && !n_present) {
-            stop(n_msg)
+          stop(n_msg)
         }
     }
     return(list(
diff --git a/R/sort_coords.R b/R/sort_coords.R
index f3847b2..cf55b27 100644
--- a/R/sort_coords.R
+++ b/R/sort_coords.R
@@ -4,8 +4,6 @@
 #' @param sumstats_dt \link[data.table]{data.table} obj of the
 #'  summary statistics file for the GWAS.
 #' @param sort_coords Whether to sort by coordinates.
-#' @param make_ordered Make CHR into an ordered factor to ensure 
-#' they go from 1-22, X, Y.
 #' @param sort_method Method to sort coordinates by: 
 #' \itemize{
 #' \item{"data.table" (default)}{Uses \link[data.table]{setorderv},
@@ -22,26 +20,26 @@
 sort_coords <- function(sumstats_dt,
                         sort_coordinates = TRUE, 
                         sort_method=c("data.table","GenomicRanges")) {
-    ### Add this to avoid confusing BiocCheck
-    CHR <- NULL
-
-    if (isTRUE(sort_coordinates)) {
-        #### Report ####
-        sort_method <- sort_method[1]
-        messager("Sorting coordinates with",paste0(shQuote(sort_method),".")) 
-        ### Double check that X and Y are uppercase
-        sumstats_dt[, CHR := gsub("x|23", "X", CHR)]
-        sumstats_dt[, CHR := gsub("y", "Y", CHR)]
-        sumstats_dt[, CHR := gsub("mt", "MT", CHR)]
-        #### Sort ####
-        if(sort_method=="data.table"){
-            sumstats_dt <- sort_coords_datatable(sumstats_dt = sumstats_dt)   
-        } else if (sort_method=="GenomicRanges"){
-            sumstats_dt <- sort_coord_genomicranges(sumstats_dt = sumstats_dt)   
-        }
-        ### Now set CHR back to character to avoid issues 
-        # when merging with other dts
-        sumstats_dt[,CHR:=as.character(CHR)]
+  ### Add this to avoid confusing BiocCheck
+  CHR <- NULL
+  
+  if (isTRUE(sort_coordinates)) {
+    #### Report ####
+    sort_method <- sort_method[1]
+    messager("Sorting coordinates with",paste0(shQuote(sort_method),".")) 
+    ### Double check that X and Y are uppercase
+    sumstats_dt[, CHR := gsub("x|23", "X", CHR)]
+    sumstats_dt[, CHR := gsub("y", "Y", CHR)]
+    sumstats_dt[, CHR := gsub("mt", "MT", CHR)]
+    #### Sort ####
+    if(sort_method=="data.table"){
+      sumstats_dt <- sort_coords_datatable(sumstats_dt = sumstats_dt)   
+    } else if (sort_method=="GenomicRanges"){
+      sumstats_dt <- sort_coord_genomicranges(sumstats_dt = sumstats_dt)   
     }
-    return(sumstats_dt)
+    ### Now set CHR back to character to avoid issues 
+    # when merging with other dts
+    sumstats_dt[,CHR:=as.character(CHR)]
+  }
+  return(sumstats_dt)
 }
diff --git a/man/sort_coords.Rd b/man/sort_coords.Rd
index 0715072..0ce376f 100644
--- a/man/sort_coords.Rd
+++ b/man/sort_coords.Rd
@@ -25,9 +25,6 @@ but much slower than the "data.table" method.}
 }}
 
 \item{sort_coords}{Whether to sort by coordinates.}
-
-\item{make_ordered}{Make CHR into an ordered factor to ensure
-they go from 1-22, X, Y.}
 }
 \value{
 Sorted sumstats_dt