modif mark_prop chi

.Rproj.user/9DAE6990/pcs/source-pane.pper

 {
-    "activeTab" : 6
+    "activeTab" : 1
 }
\ No newline at end of file

.Rproj.user/9DAE6990/pcs/windowlayoutstate.pper

 {
     "left" : {
-        "panelheight" : 1271,
-        "splitterpos" : 533,
-        "topwindowstate" : "NORMAL",
-        "windowheight" : 1309
+        "panelheight" : 583,
+        "splitterpos" : 244,
+        "topwindowstate" : "MAXIMIZE",
+        "windowheight" : 621
     },
     "right" : {
         "panelheight" : 1271,
-        "splitterpos" : 804,
+        "splitterpos" : 803,
         "topwindowstate" : "NORMAL",
         "windowheight" : 1309
     }

.Rproj.user/9DAE6990/pcs/workbench-pane.pper

 {
-    "TabSet1" : 3,
+    "TabSet1" : 0,
     "TabSet2" : 4,
     "TabZoom" : {
     }

.Rproj.user/9DAE6990/sources/prop/52B275C1

 {
-    "cursorPosition" : "16,28",
-    "scrollLine" : "0"
+    "cursorPosition" : "70,29",
+    "scrollLine" : "40"
 }
\ No newline at end of file

.Rproj.user/9DAE6990/sources/prop/63BDD9CA

+{
+}
\ No newline at end of file

.Rproj.user/9DAE6990/sources/prop/B92E179B

 {
-    "cursorPosition" : "135,15",
-    "last_setup_crc32" : "",
-    "scrollLine" : "111"
+    "cursorPosition" : "114,53",
+    "last_setup_crc32" : "E69463565bfca283",
+    "scrollLine" : "110"
 }
\ No newline at end of file

.Rproj.user/9DAE6990/sources/prop/INDEX

@@ -22,3 +22,4 @@
 ~%2Fstuart_package%2Fstuart%2Fdoc%2FstuaRt.R="65312719"
 ~%2Fstuart_package%2Fstuart%2Fvignettes%2FstuaRt.R="EBD625D2"
 ~%2Fstuart_package%2Fstuart%2Fvignettes%2FstuaRt.Rmd="D602FFE4"
+~%2Fstuart_package%2Fstuart_old%2FR%2Fmark_prop.R="63BDD9CA"

.Rproj.user/9DAE6990/sources/per/t/1656F55 → .Rproj.user/9DAE6990/sources/s-E6946356/1656F55

@@ -5,10 +5,10 @@
     "dirty" : false,
     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "1203844341",
+    "hash" : "0",
     "id" : "1656F55",
-    "lastKnownWriteTime" : 1622640147,
-    "last_content_update" : 1622640147,
+    "lastKnownWriteTime" : 1623060553,
+    "last_content_update" : 1623060553,
     "path" : "~/Documents/PhD/stuart_R/stuart/R/geno_strains.R",
     "project_path" : "R/geno_strains.R",
     "properties" : {

.Rproj.user/9DAE6990/sources/per/t/42D37312 → .Rproj.user/9DAE6990/sources/s-E6946356/42D37312

@@ -5,20 +5,20 @@
     "dirty" : false,
     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "3094972460",
+    "hash" : "0",
     "id" : "42D37312",
-    "lastKnownWriteTime" : 1623061718,
-    "last_content_update" : 1623061718577,
+    "lastKnownWriteTime" : 1623086204,
+    "last_content_update" : 1623086204670,
     "path" : "~/Documents/PhD/stuart_R/stuart/R/mark_prop.R",
     "project_path" : "R/mark_prop.R",
     "properties" : {
-        "cursorPosition" : "16,28",
-        "scrollLine" : "0"
+        "cursorPosition" : "70,29",
+        "scrollLine" : "40"
     },
     "read_only" : false,
     "read_only_alternatives" : [
     ],
-    "relative_order" : 9,
+    "relative_order" : 2,
     "source_on_save" : false,
     "source_window" : "",
     "type" : "r_source"

.Rproj.user/9DAE6990/sources/per/t/42D37312-contents → .Rproj.user/9DAE6990/sources/s-E6946356/42D37312-contents

@@ -14,10 +14,9 @@
 
 #### mark_prop ####
 ## excludes markers depending on proportions of homo/hetorozygous
-## to modify with chisq.test
-mark_prop <- function(tab,cross,homo=NA,hetero=NA,na=0.5){
+mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
   #calculate total number of individuals genotyped for each marker
-  tab <- tab %>% mutate(n_geno = tab %>% select(n_HM1,n_HM2,n_HT) %>% rowSums(na.rm=TRUE))
+  tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
 
   #calculate proportion of each genotype
   tab <- tab %>% mutate(p_HM1 = n_HM1/n_geno)
@@ -25,27 +24,50 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,na=0.5){
   tab <- tab %>% mutate(p_HT = n_HT/n_geno)
   tab <- tab %>% mutate(p_NA = n_NA/(n_geno+n_NA))
 
+  #stock colnames to join
+  names <- colnames(tab)
+
+
   #stop if cross != "F2" or "N2"
   if(!cross %in% c("F2","N2")){
     stop("Cross must be F2 or N2")
   }
 
-  #stop if no value for "homo" for F2 cross
-  if(cross=="F2" & (is.na(homo)==TRUE | is.na(hetero)==TRUE)){
-    stop("Arguments homo and hetero must be specified for F2 crosses")
+  #stop of homo&hetero or pval not specified
+  if((is.na(homo)==TRUE | is.na(hetero)==TRUE) & is.na(pval)==TRUE){
+    stop("Arguments homo and hetero or argument pval must be specified")
   }
 
-  #stop if no value for "homo" and "hetero" for N2 cross
-  if(cross=="N2" & (is.na(homo)==TRUE | is.na(hetero)==TRUE)){
-    stop("Arguments homo and hetero must be specified for N2 crosses")
+
+
+  #stop with prop of na
+  tab <- tab %>%
+    mutate(exclude_prop=case_when(p_NA > na ~ 1,
+                                  T ~ 0))
+
+  #stop with prop of homo/hetero
+  if(is.na(pval)==TRUE){
+    tab <- tab %>%
+      mutate(exclude_prop=case_when(p_NA > na ~ 1,
+                                    cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
+                                    cross=="N2" & (p_HM1 < homo | p_HT < hetero) ~ 1,
+                                    T ~ exclude_prop
+      ))
   }
 
-  #exclude markers according to proportion of na
-  tab <- tab %>% mutate(exclude_prop=case_when(p_NA > na ~ 1, #exclude markers according to proportion of na
-                                               cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1, #exclude markers according to proportion of homozygous individuals for F2 cross
-                                               cross=="N2" & (p_HM1 < homo | p_HT < hetero) ~ 1, #exclude markers according to proportion of homozygous and heterozygous individuals for N2 cross
-                                               T ~ 0))
+  #stop with pval chisq.test
+  ## NEED TO ADD THIS FILTER IF CROSS = N2
+  if(is.na(pval)==FALSE){
+
+    tab <- tab %>% filter(p_NA != 1) %>% rowwise() %>%
+      mutate(.,chi_pval = tibble(n_HM1,n_HM2,n_HT) %>%
+               chisq.test(p=c(0.25,0.25,0.5)) %>% .$p.value) %>%
+      full_join(.,tab,by=names)
+
+    tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+                                                 T ~ exclude_prop))
+  }
 
-  tab <- tab %>% select(-c(p_HM1,p_HM2,p_HT,p_NA,n_geno))
+  tab <- tab %>% select(names)
   return(tab)
 }

.Rproj.user/9DAE6990/sources/per/t/45D91D58 → .Rproj.user/9DAE6990/sources/s-E6946356/45D91D58

@@ -5,7 +5,7 @@
     "dirty" : false,
     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "1139135974",
+    "hash" : "0",
     "id" : "45D91D58",
     "lastKnownWriteTime" : 1622648301,
     "last_content_update" : 1622648301329,
@@ -18,7 +18,7 @@
     "read_only" : false,
     "read_only_alternatives" : [
     ],
-    "relative_order" : 11,
+    "relative_order" : 9,
     "source_on_save" : false,
     "source_window" : "",
     "type" : "r_source"

.Rproj.user/9DAE6990/sources/per/t/65C9B72B → .Rproj.user/9DAE6990/sources/s-E6946356/65C9B72B

@@ -5,10 +5,10 @@
     "dirty" : false,
     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "1762622592",
+    "hash" : "0",
     "id" : "65C9B72B",
-    "lastKnownWriteTime" : 1622642120,
-    "last_content_update" : 1622642120783,
+    "lastKnownWriteTime" : 1623060553,
+    "last_content_update" : 1623060553,
     "path" : "~/Documents/PhD/stuart_R/stuart/R/tab_mark.R",
     "project_path" : "R/tab_mark.R",
     "properties" : {

.Rproj.user/9DAE6990/sources/s-E6946356/6DCC955A

+{
+    "collab_server" : "",
+    "contents" : "",
+    "created" : 1623083300385.000,
+    "dirty" : false,
+    "encoding" : "",
+    "folds" : "",
+    "hash" : "0",
+    "id" : "6DCC955A",
+    "lastKnownWriteTime" : 140320379993736,
+    "last_content_update" : 1623083300385,
+    "path" : null,
+    "project_path" : null,
+    "properties" : {
+        "cacheKey" : "FFFA47E6",
+        "caption" : "test_tab",
+        "contentUrl" : "grid_resource/gridviewer.html?env=&obj=test_tab&cache_key=FFFA47E6",
+        "displayedObservations" : "20",
+        "environment" : "",
+        "expression" : "test_tab",
+        "object" : "test_tab",
+        "preview" : "0",
+        "totalObservations" : "20",
+        "variables" : "9"
+    },
+    "read_only" : false,
+    "read_only_alternatives" : [
+    ],
+    "relative_order" : 12,
+    "source_on_save" : false,
+    "source_window" : "",
+    "type" : "r_dataframe"
+}
\ No newline at end of file

.Rproj.user/9DAE6990/sources/per/t/76AC3EC → .Rproj.user/9DAE6990/sources/s-E6946356/76AC3EC

@@ -5,7 +5,7 @@
     "dirty" : false,
     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "143869640",
+    "hash" : "0",
     "id" : "76AC3EC",
     "lastKnownWriteTime" : 1623060553,
     "last_content_update" : 1623060553,
@@ -18,7 +18,7 @@
     "read_only" : false,
     "read_only_alternatives" : [
     ],
-    "relative_order" : 7,
+    "relative_order" : 6,
     "source_on_save" : false,
     "source_window" : "",
     "type" : "r_source"