update_perfect_GWASpoly_positions

.Rhistory

@@ -10,3 +10,7 @@ devtools::document()
 devtools::document()
 devtools::document()
 devtools::document()
+genomic_pos = read.csv("https://raw.githubusercontent.com/jeekinlau/RoseArrayTools/master/data/perfect_fits_saintoyant.csv", header = T)
+View(genomic_pos)
+roxygen2::roxygenise()
+devtools::install_github("jeekinlau/RoseArrayTools")

.Rproj.user/036DA200/pcs/windowlayoutstate.pper

@@ -7,7 +7,7 @@
     },
     "right": {
         "splitterpos": 666,
-        "topwindowstate": "MAXIMIZE",
+        "topwindowstate": "NORMAL",
         "panelheight": 1071,
         "windowheight": 1109
     }

.Rproj.user/036DA200/pcs/workbench-pane.pper

@@ -1,5 +1,5 @@
 {
     "TabSet1": 0,
-    "TabSet2": 0,
+    "TabSet2": 2,
     "TabZoom": {}
 }

R/fitpoly_to_gwaspoly_input.R

@@ -7,7 +7,7 @@
 #' @return a .csv file that has the added columns of genome position and LG of markers. Will contain markers with no known location at bottom of file.
 #'
 #' @export fitPoly_to_GWASpoly_input
-#'
+#' @export fitpoly_to_GWASpoly_input_perfect
 #'
 #'
 #'
@@ -36,3 +36,27 @@ fitPoly_to_GWASpoly_input <- function(input_file){
   write.csv(final,paste0(input_file_name,"_GWAS_ready.csv"),row.names = F)
   print("done")
 }
+
+
+
+fitPoly_to_GWASpoly_input_perfect <- function(input_file){
+  input_file_name = gsub(".csv","",input_file)
+  file = read.csv(input_file)
+  genomic_pos = read.csv("https://raw.githubusercontent.com/jeekinlau/RoseArrayTools/master/data/perfect_fits_saintoyant.csv", header = T)
+
+  temp_names = colnames(file)
+  temp_names[1] = "Marker"
+  colnames(file) = temp_names
+
+  merged = merge(file,genomic_pos, by="Marker", all=T)
+
+  merged_genotypes = merged[,-which(colnames(merged)%in%c("Marker","LG","Position"))]
+
+  final = cbind(merged$Marker,  merged$LG, merged$Position, merged_genotypes)
+  final_colnames <- colnames(final)
+  final_colnames[1:3] = c("Marker", "Chrom", "Position")
+  colnames(final) = final_colnames
+  final = final[order(final$Chrom, final$Position),]
+  write.csv(final,paste0(input_file_name,"_GWAS_ready.csv"),row.names = F)
+  print("done")
+}