diff --git a/.Rproj.user/9DAE6990/pcs/source-pane.pper b/.Rproj.user/9DAE6990/pcs/source-pane.pper
index d3d70fa0c6a708df53d33b21eeb319f4067fd72c..3249574fb10b23a53547595769fe33dcbefc247e 100644
--- a/.Rproj.user/9DAE6990/pcs/source-pane.pper
+++ b/.Rproj.user/9DAE6990/pcs/source-pane.pper
@@ -1,3 +1,3 @@
 {
-    "activeTab" : 6
+    "activeTab" : 2
 }
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diff --git a/.Rproj.user/9DAE6990/pcs/windowlayoutstate.pper b/.Rproj.user/9DAE6990/pcs/windowlayoutstate.pper
index 19ed75d204afa8df78f1acd69e1abe929ed916af..7f81dbca9534909c28629955d65a0cd2b42efead 100644
--- a/.Rproj.user/9DAE6990/pcs/windowlayoutstate.pper
+++ b/.Rproj.user/9DAE6990/pcs/windowlayoutstate.pper
@@ -1,14 +1,14 @@
 {
     "left" : {
-        "panelheight" : 762,
-        "splitterpos" : 199,
+        "panelheight" : 1402,
+        "splitterpos" : 366,
         "topwindowstate" : "NORMAL",
-        "windowheight" : 800
+        "windowheight" : 1440
     },
     "right" : {
-        "panelheight" : 762,
-        "splitterpos" : 479,
+        "panelheight" : 1402,
+        "splitterpos" : 882,
         "topwindowstate" : "NORMAL",
-        "windowheight" : 800
+        "windowheight" : 1440
     }
 }
\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/pcs/workbench-pane.pper b/.Rproj.user/9DAE6990/pcs/workbench-pane.pper
index b15bf239a65db2c71879040ca11430d12ee3e636..b9fcffa7969da03fcda0fc797bd2d2041388fd6e 100644
--- a/.Rproj.user/9DAE6990/pcs/workbench-pane.pper
+++ b/.Rproj.user/9DAE6990/pcs/workbench-pane.pper
@@ -1,6 +1,6 @@
 {
-    "TabSet1" : 3,
-    "TabSet2" : 0,
+    "TabSet1" : 1,
+    "TabSet2" : 3,
     "TabZoom" : {
     }
 }
\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/persistent-state b/.Rproj.user/9DAE6990/persistent-state
index 598ea69db312e503afab921bf885574c2cacf39b..acadc07ed32e177fb45b81a1bba3c8c166f5ac91 100644
--- a/.Rproj.user/9DAE6990/persistent-state
+++ b/.Rproj.user/9DAE6990/persistent-state
@@ -1,6 +1,6 @@
 build-last-errors="[]"
 build-last-errors-base-dir="~/Documents/PhD/stuart_package/stuart/"
-build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source stuart\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* installing *source* package ‘stuart’ ...\\n\",\"type\":1},{\"output\":\"** using staged installation\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** data\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** moving datasets to lazyload DB\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** inst\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** byte-compile and prepare package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** installing vignettes\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from temporary location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from final location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\",\"type\":1},{\"output\":\"* DONE (stuart)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
+build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source stuart\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’\\n\",\"type\":1},{\"output\":\"* installing *source* package ‘stuart’ ...\\n\",\"type\":1},{\"output\":\"** using staged installation\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** data\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** moving datasets to lazyload DB\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** inst\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** byte-compile and prepare package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** installing vignettes\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from temporary location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from final location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\",\"type\":1},{\"output\":\"* DONE (stuart)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
 compile_pdf_state="{\"errors\":[],\"output\":\"\",\"running\":false,\"tab_visible\":false,\"target_file\":\"\"}"
 files.monitored-path=""
 find-in-files-state="{\"handle\":\"\",\"input\":\"\",\"path\":\"\",\"regex\":true,\"results\":{\"file\":[],\"line\":[],\"lineValue\":[],\"matchOff\":[],\"matchOn\":[]},\"running\":false}"
diff --git a/.Rproj.user/9DAE6990/rmd-outputs b/.Rproj.user/9DAE6990/rmd-outputs
index 97de97abbe9bcd117600615a5db201d40e05685f..3da60b5006c8030c8adc1ba14e9eb9b0bfb4a27c 100644
--- a/.Rproj.user/9DAE6990/rmd-outputs
+++ b/.Rproj.user/9DAE6990/rmd-outputs
@@ -1,5 +1,5 @@
-/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpZZZ4WE/preview-31873a42c16d.dir/stuaRt.html
-/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/Rtmp3VMULh/preview-1ced48fe920c.dir/stuaRt.html
+/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpbddlPL/preview-1b515493e142.dir/stuart.html
+
 /private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpNme5vw/preview-4c4321234d03.dir/stuaRt.html
 /private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpZZZ4WE/preview-3187564b41ab.dir/stuaRt.html
 
diff --git a/.Rproj.user/9DAE6990/sources/prop/INDEX b/.Rproj.user/9DAE6990/sources/prop/INDEX
index c8854a683fb80042b68a0a40757c095808f8c78e..736b651a028fd32e72bac0befaac79d7666e7a7b 100644
--- a/.Rproj.user/9DAE6990/sources/prop/INDEX
+++ b/.Rproj.user/9DAE6990/sources/prop/INDEX
@@ -1,4 +1,5 @@
 %2FVolumes%2F%40Mouselab%2FZika%2FBackcross%2FGeno%2FBC_01.71_stuart.Rmd="73DD6D1F"
+%2FVolumes%2F%40Mouselab%2FZika%2FF2%2FF2_B6.CC001%2FQUGA%2FQUGA.Rmd="D7285907"
 ~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2FDESCRIPTION="A58355B1"
 ~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2FR%2Fgeno_strains.R="430FE7D7"
 ~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2FR%2Fmark_allele.R="58D83345"
diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
index 9a8495e543e3ce6c3f75c2c7691e3d8a244cee85..3457e0eb55255067b49abb12c6163d7243530939 100644
--- a/.Rproj.user/shared/notebooks/paths
+++ b/.Rproj.user/shared/notebooks/paths
@@ -10,3 +10,4 @@
 /Users/mariebourdon/Documents/PhD/stuart_package/stuart/man/mark_prop.Rd="893B273D"
 /Users/mariebourdon/Documents/PhD/stuart_package/stuart/vignettes/stuaRt.Rmd="DA6206CB"
 /Users/mariebourdon/Documents/PhD/stuart_package/stuart/vignettes/stuart.Rmd="54D793B9"
+/Volumes/@Mouselab/Zika/F2/F2_B6.CC001/QUGA/QUGA.Rmd="7EACFFBF"
diff --git a/R/mark_prop.R b/R/mark_prop.R
index a10ec6b4c252ca83fc3b8af10a6b5e1c74011bbd..0d756dfddafaae10d75b2cb2f11f383c04524015 100755
--- a/R/mark_prop.R
+++ b/R/mark_prop.R
@@ -26,7 +26,7 @@
 
 #### mark_prop ####
 ## excludes markers depending on proportions of homo/hetorozygous
-mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NULL,heteroX=NULL,na=0.5){
+mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NULL,heteroX=NULL){
   #calculate total number of individuals genotyped for each marker
   tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
 
@@ -59,8 +59,7 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NUL
   tab <- tab %>% mutate(p_NA = n_NA/(n_geno+n_NA))
 
   tab <- tab %>%
-    mutate(exclude_prop=case_when(p_NA > na ~ 1,
-                                  T ~ 0))
+    mutate(exclude_prop=0)
 
   #stock colnames to join
   names <- colnames(tab)
@@ -73,8 +72,7 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NUL
     tab <- tab %>% mutate(p_HT = n_HT/n_geno)
 
     tab <- tab %>%
-      mutate(exclude_prop=case_when(p_NA > na ~ 1,
-                                    !chr %in% c("X","Y","M") & cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
+      mutate(exclude_prop=case_when(!chr %in% c("X","Y","M") & cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
                                     !chr %in% c("X","Y","M") & cross=="N2" & ((p_HM2 == 0 & p_HM1 < homo) |
                                                                                 (p_HM1 == 0 & p_HM2 < homo) |
                                                                                 (p_HT < hetero) |
@@ -88,8 +86,8 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NUL
         mutate(exclude_prop=case_when(chr == "X" & p_HM1 >= p_HM2 & !between(p_HM1,homo1X[1],homo1X[2]) ~ 1,
                                       chr == "X" & p_HM2 > p_HM1 & !between(p_HM2,homo1X[1],homo1X[2]) ~ 1,
                                       T ~ exclude_prop
-                                      )
-               )
+        )
+        )
     }
 
     if(is.null(homo2X)==FALSE){
@@ -97,16 +95,16 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NUL
         mutate(exclude_prop=case_when(chr == "X" & p_HM1 >= p_HM2 & !between(p_HM2,homo2X[1],homo2X[2]) ~ 1,
                                       chr == "X" & p_HM2 > p_HM1 & !between(p_HM1,homo2X[1],homo2X[2]) ~ 1,
                                       T ~ exclude_prop
-                                      )
-              )
+        )
+        )
     }
 
     if(is.null(heteroX)==FALSE){
       tab <- tab %>%
         mutate(exclude_prop=case_when(chr == "X" & p_HM1 >= p_HM2 & !between(p_HT,heteroX[1],heteroX[2]) ~ 1,
                                       T ~ exclude_prop
-                                      )
-              )
+        )
+        )
     }
 
     #exclude with pval chisq.test
diff --git a/stuart_1.0.5.tar.gz b/stuart_1.0.5.tar.gz
index ffe005a89d01aa88b963831fc718ece038c1e233..c74c1bff8ed4a413106168806a91ca21aae2f4be 100644
Binary files a/stuart_1.0.5.tar.gz and b/stuart_1.0.5.tar.gz differ
diff --git a/vignettes/screenshot_newmap.png b/vignettes/screenshot_newmap.png
new file mode 100644
index 0000000000000000000000000000000000000000..00a914edccfb006c288eb42009782801e027dbb5
Binary files /dev/null and b/vignettes/screenshot_newmap.png differ
diff --git a/vignettes/stuart.Rmd b/vignettes/stuart.Rmd
index 13fb74af52072740a5b27233cafa45ddfb9d85be..7ab93c63ac0ac60ee417340aa4fb6a3b3514d8ea 100755
--- a/vignettes/stuart.Rmd
+++ b/vignettes/stuart.Rmd
@@ -52,7 +52,19 @@ Here, we will present an example of the use of stuart with results of a F2 cross
 
 The genotype data frame must contain a first column with marker names, a second column with sample IDs, a third column with the first allele and a fourth column with the second allele. This format corresponds to the MUGA results. If your data differ, make sure to have these columns in this order.
 
-We load the result of Neogen genotyping: `genos` (only useful columns with marker name, sample ID and alleles were kept) and the phenotype dataset produced by the lab: `phenos`.
+You can load your genotype data with base R function `read.table()` or with `readr::read_tsv()` function. You have to skip the first lines with the header.
+
+* `read.table("path/to/genotype_data.txt",sep = "\t",skip=9,header=TRUE)`
+
+* `readr::read_tsv("path/to/genotype_data.txt",skip=9)`
+
+The phenotype data produced by the lab must have the following format: one line per individual, one column per phenotype. The first column must be the identification number of each individual.
+
+You can load your phenotype data depending on its format with `read.table()` or `readr::read_tsv()` for txt files, `read.table()` or `readr::read_csv()` for csv files, `read_excel::read_xls` or `read_excel::read_xlsx` for excel files. 
+
+Here, we load the result of Neogen genotyping: `genos` (only useful columns with marker name, sample ID and alleles were kept) and the phenotype dataset produced by the lab: `phenos`, directly available in the package.
+
+
 
 
 ```{r load}
@@ -118,7 +130,7 @@ tab2 <- mark_na(stuart_tab)
 Then, we can use `mark_match()` function. Here, the parental strains were genotyped with the F2 individuals, but it can happen that you use previous genotyping results for the parental strains. `mark_match()` function excludes markers that are in your genotype file but not in the reference genotype dataset. We recomend using this function as the chip used for genotyping may change.
 
 ```{r mark_match}
-tab2 <- mark_match(stuart_tab,ref=strains)
+tab2 <- mark_match(tab2,ref=strains)
 tab2 %>% filter(exclude_match==1) %>% print.data.frame()
 ```
 
@@ -135,7 +147,7 @@ head(tab2) %>% print.data.frame()
 
 ### mark_prop
 
-The `mark_prop()` function can be used to filter markers depending on the proportion of each genotype. Here, we have a F2 and we use `homo=0.1, hetero=0.1`  so the function will exclude all markers with less than 10% of each genotype. Moreover, this function allows to filter marker depending on the proportion on non genotyped animals. By defaults, markers for which more than 50% of individuals were not genotyped. For chromosome X, we use the `homo=0.1, hetero=0.1`
+The `mark_prop()` function can be used to filter markers depending on the proportion of each genotype. Here, we have a F2 and we use `homo=0.1, hetero=0.1`  so the function will exclude all markers with less than 10% of each genotype. For chromosome X, we use the `homo=0.1, hetero=0.1`
 
 ```{r mark_prop_ex_homo}
 tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1,homo1X=c(0.1,1),homo2X=c(0.1,1),heteroX=c(0.1,1))
@@ -222,6 +234,12 @@ To avoid the issues with these situations, you can use the `parNH=FALSE` argumen
 We rather advise you to keep these markers and identify possible problematic markers with `mark_estmap()` and exlude them. 
 
 
-If there are still some markers that need to be excluded after all these steps, you have two possibilities to exclude them. First, you can drop these markers in the cross object with `qtl::drop.markers()`, or if you prefere to have a correct CSV object that can always be used for QTL analysis, you can delete these markers in the marker tab and create a new cross file with `write_rqtl()`:
+If there are still some markers that need to be excluded after all these steps, you have two possibilities to exclude them. First, you have to identify the name of these markers by looking at the `newmap` object as follow : in RStudio, click on this objectin the Environment to view it, then click on the arrow on the left of the desired chromosome. Each chromosome is a named vector that is visible here in two columns: one with the name of the marker, and one with the calculated position of the marker. This is how you can detect markers that present a huge gap with the previous and the following marker.
+
+You can see an example for the stuart_newmap object in the following screen shot:
+
+![screenchot_newmap](screenshot_newmap.png)
+
+You can drop these markers in the cross object with `qtl::drop.markers()`, or if you prefere to have a correct CSV object that can always be used for QTL analysis, you can delete these markers in the marker tab and create a new cross file with `write_rqtl()`.