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+++ b/.Rproj.user/9DAE6990/pcs/source-pane.pper
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rename to .Rproj.user/9DAE6990/sources/per/t/42D37312-contents
index a0827e8c27b02c9d65a6cc3af34cf595f50a5840..8af6e843dc7d88ac3724cf1c46fde5ba9b43f416 100644
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+++ b/.Rproj.user/9DAE6990/sources/per/t/42D37312-contents
@@ -14,6 +14,7 @@
 
 #### 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){
   #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))
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index 0000000000000000000000000000000000000000..4c067597f326f93a2178a77bfffe89df9d1ceed1
--- /dev/null
+++ b/.Rproj.user/9DAE6990/sources/prop/DB7C2433
@@ -0,0 +1,4 @@
+{
+    "cursorPosition" : "20,46",
+    "scrollLine" : "0"
+}
\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/sources/prop/E7505D7B b/.Rproj.user/9DAE6990/sources/prop/E7505D7B
new file mode 100644
index 0000000000000000000000000000000000000000..a5638714b0481f1423ea85365c8af64243a71277
--- /dev/null
+++ b/.Rproj.user/9DAE6990/sources/prop/E7505D7B
@@ -0,0 +1,4 @@
+{
+    "cursorPosition" : "9,51",
+    "scrollLine" : "0"
+}
\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/sources/prop/INDEX b/.Rproj.user/9DAE6990/sources/prop/INDEX
index 16f98885be4bba0b41bed600c49af1738abd995d..eb9f95ac9ea85eec475733598ad68958be13be45 100644
--- a/.Rproj.user/9DAE6990/sources/prop/INDEX
+++ b/.Rproj.user/9DAE6990/sources/prop/INDEX
@@ -1,3 +1,13 @@
+~%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"
+~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2FR%2Fmark_match.R="DB7C2433"
+~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2FR%2Fmark_poly.R="E7505D7B"
+~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2FR%2Fmark_prop.R="52B275C1"
+~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2FR%2Fstuart_tab-data.R="524B281F"
+~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2FR%2Ftab_mark.R="C4894908"
+~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2FR%2Fwrite_rqtl.R="B873B132"
+~%2FDocuments%2FPhD%2Fstuart_R%2Fstuart%2Fvignettes%2FstuaRt.Rmd="B92E179B"
 ~%2Fstuart_package%2Fstuart%2FDESCRIPTION="BEB7232"
 ~%2Fstuart_package%2Fstuart%2FNAMESPACE="AE613167"
 ~%2Fstuart_package%2Fstuart%2FR%2Fgeno_strains.R="8F7B714A"
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/17AE345-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/17AE345-contents
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/47AFB64-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/47AFB64-contents
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/4A9D04E-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/4A9D04E-contents
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/6B5DE0D4-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/6B5DE0D4-contents
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/7E4482C6-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/7E4482C6-contents
deleted file mode 100644
index fd50eb0ea6a1188c1f619aa7510b6b276c9c2895..0000000000000000000000000000000000000000
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/7E4482C6-contents
+++ /dev/null
@@ -1,8 +0,0 @@
-#' Data frame with miniMUGA genotyping of F2 individuals and parental strains
-#'
-#' A dataset containing the genotypes of 176 F2 individuals
-#'
-#' @format A data frame with 2002493 observations of 11 variables
-
-
-"genos"
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/806AAC34-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/806AAC34-contents
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/81311FDE-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/81311FDE-contents
deleted file mode 100644
index 612c27db930cb54d481e09a9a7ab5efd4912420f..0000000000000000000000000000000000000000
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/81311FDE-contents
+++ /dev/null
@@ -1,137 +0,0 @@
-#' @title Create of the summary table for all markers from the genotype data frame
-#'
-#' @description This function creates a table with all the markers that were genotyped in the array, the alleles for these markers, the number of homozygous and heterozygous animals, as well as the number of non genotyped animals.
-#' @param geno data frame with the genotyping results for your cross
-#'
-#' @import dplyr
-#' @import tidyr
-#'
-#' @export
-#'
-
-#### tab_mark function ####
-## create table with markers and counts
-tab_mark <- function(geno){
-  #create geno column in geno df
-  geno <- geno %>% unite(Geno,c("Allele1...Forward","Allele2...Forward"),sep="",remove=FALSE)
-
-  #recode genotypes to have all heterozygous encoded the same way (ex: only "AT", no "TA")
-  geno <- geno %>% mutate(Geno=recode(Geno,
-                                      "TA" = "AT",
-                                      "GA" = "AG",
-                                      "CA" = "AC",
-                                      "GT" = "TG",
-                                      "CT" = "TC",
-                                      "GC" = "CG"))
-
-
-  #create df with counts for each genotype
-  df_count <- tibble(SNP.Name = as.character(unique(geno$SNP.Name)),
-                     Allele_1 = NA,
-                     Allele_2 = NA,
-                     n_HM1 = NA,
-                     n_HM2 = NA,
-                     n_HT = NA,
-                     n_NA = NA)
-
-
-  ## loop to count genotype
-  for(i in df_count$SNP.Name){
-    #extract alleles for each marker
-    Alleles <- geno %>% filter(SNP.Name==i) %>%
-      select(c(SNP.Name,Sample.ID,Geno,Allele1...Forward,Allele2...Forward)) %>%
-      pivot_longer(c(Allele1...Forward,Allele2...Forward),names_to="Allele_name",values_to="Allele") %>%
-      distinct(Allele) %>% filter(Allele != "-")
-    Alleles <- as.factor(paste(Alleles$Allele))
-
-    #sort alleles
-    Alleles <- factor(Alleles,levels=c("A","T","C","G"))
-    Alleles <- sort(Alleles)
-
-    #add alleles and counts, only for markers with alleles (not markers with no genotyped ind)
-    if(all(rapportools::is.empty(Alleles))==FALSE){
-
-      #add alleles to df_count
-      df_count <- df_count %>% mutate(Allele_1 = ifelse(SNP.Name == i,
-                                                        paste(Alleles[1]), Allele_1))
-
-
-
-      #count for homozygous for allele 1
-      n1 <- geno %>% filter(SNP.Name==i) %>%
-        filter(Geno == paste(Alleles[1],Alleles[1],sep="")) %>%
-        summarise(n=n())
-
-
-      #add count for homozygous for allele 1 to df_count
-      df_count <- df_count %>% mutate(n_HM1 = ifelse(SNP.Name == i,
-                                                     n1$n, n_HM1))
-
-
-    }
-
-    #if marker not polymorphic
-    if(is.na(Alleles[2])==TRUE){
-      #NA as Allele_2
-      df_count <- df_count %>% mutate(Allele_2 = ifelse(SNP.Name == i,
-                                                        NA, Allele_2))
-
-      #NA as n_HM2
-      df_count <- df_count %>% mutate(n_HM2 = ifelse(SNP.Name == i,
-                                                     NA, n_HM2))
-
-      #NA as n_HT
-      df_count <- df_count %>% mutate(n_HT = ifelse(SNP.Name == i,
-                                                    NA, n_HT))
-    } else {
-      #add alleles to df_count
-      df_count <- df_count %>% mutate(Allele_2 = ifelse(SNP.Name == i,
-                                                        paste(Alleles[2]), Allele_2))
-
-
-      #count for homozygous for allele 2
-      n2 <- geno %>% filter(SNP.Name==i) %>%
-        filter(Geno == paste(Alleles[2],Alleles[2],sep="")) %>%
-        summarise(n=n())
-
-      #add count for homozygous for allele 1 to df_count
-      df_count <- df_count %>% mutate(n_HM2 = ifelse(SNP.Name == i,
-                                                     n2$n, n_HM2))
-
-
-      #count for heterozygous
-      n3 <- geno %>% filter(SNP.Name==i) %>%
-        filter(Geno == paste(Alleles[1],Alleles[2],sep="")) %>%
-        summarise(n=n())
-
-
-      #add count for homozygous for allele 1 to df_count
-      df_count <- df_count %>% mutate(n_HT = ifelse(SNP.Name == i,
-                                                    n3$n, n_HT))
-
-
-    }
-
-    #count for NA
-    n4 <- geno %>% filter(SNP.Name==i) %>%
-      filter(Geno == "--" |
-               Geno == paste(Alleles[1],"-",sep="") | Geno == paste(Alleles[2],"-",sep="") |
-               Geno == paste("-",Alleles[1],sep="") | Geno == paste("-",Alleles[2],sep="")) %>%
-      summarise(n=n())
-
-    #add count for NA to df_count
-    df_count <- df_count %>% mutate(n_NA = ifelse(SNP.Name == i,
-                                                  n4$n, n_NA))
-  }
-  #change class of counts as numeric :
-  df_count$n_HM1 <- df_count$n_HM1 %>% as.numeric()
-  df_count$n_HM2 <- df_count$n_HM2 %>% as.numeric()
-  df_count$n_HT <- df_count$n_HT %>% as.numeric()
-  df_count$n_NA <- df_count$n_NA %>% as.numeric()
-
-  #add 0 for null counts
-  df_count <- df_count %>% mutate_at(.vars=vars(n_HM1,n_HM2,n_HT,n_NA),~replace(., is.na(.), 0))
-
-  #return
-  return(df_count)
-}
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/8DB3123E-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/8DB3123E-contents
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/907DF1D3-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/907DF1D3-contents
deleted file mode 100644
index d4104d0f3af4780745e4939ce649d7e90e8c995e..0000000000000000000000000000000000000000
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/907DF1D3-contents
+++ /dev/null
@@ -1,55 +0,0 @@
-#' @title Create haplotype for a new mouse strain into a reference dataframe
-#'
-#' @description This functions adds columns for parental strains used in the cross in the annotation data frame, from the genotype data frame in which one or several animal of the parental strains were genotyped.
-#' If several animals of one strain were genotyped, a consensus is created from these animals.
-#' The consensus is created as follow : if the indivuals carry the same allele, this allele is kept, otherwise, the allele is noted as "N". If individuals show residual heterozygosity, it is encoded as "H".
-#' @param ref data frame with the reference genotypes of mouse lines
-#' @param geno data frame with the genotyping results for your cross from miniMUGA array
-#' @param par1 first parental strain used in the cross, the name must be written as in the geno data frame
-#' @param par2 second parental strain used in the cross, the name must be written as in the geno data frame
-#' @param name1 name of the first parental strain to use as the column name in the ref data frame
-#' @param name2 name of the second parental strain to use as the column name in the ref data frame
-#'
-#' @import dplyr
-#' @import tidyr
-#'
-#' @export
-#'
-geno_strains <- function(ref,geno,par1,par2,name1,name2){
-  #rename df columns
-  geno <- geno %>% rename("marker"=1,
-                          "id"=2,
-                          "allele_1"=3,
-                          "allele_2"=4)
-
-
-  #recode genotypes from 2 alleles to 1
-  geno <- geno %>% mutate_all(as.character)
-  geno <- geno %>% filter(id %in% c(par1,par2))
-  geno <- geno %>% mutate(Geno=case_when(allele_1 == "-" | allele_2 == "-" ~ "N",
-                                         allele_1 == allele_2 ~ allele_1,
-                                         allele_1 %in% c("A","T","G","C") & allele_2 %in% c("A","T","G","C") ~ "H"))
-
-  geno <- geno %>% select(marker,id,Geno) %>% pivot_wider(names_from = id, values_from = Geno)
-
-
-  #create consensus
-  if(length(par1)!=1){
-    geno <- geno %>% mutate(parent1 = ifelse(!!sym(par1[1])==!!sym(par1[2]),!!sym(par1[1]),"N"))
-  } else {
-    geno <- geno %>% rename(parent1=!!sym(par1[1]))
-  }
-
-  if(length(par2)!=1){
-    geno <- geno %>% mutate(parent2 = ifelse(!!sym(par2[1])==!!sym(par2[2]),!!sym(par2[1]),"N"))
-  } else {
-    geno <- geno %>% rename(parent2=!!sym(par2[1]))
-  }
-
-  geno <- geno %>% select(marker,parent1,parent2)
-  colnames(geno) <- c("marker",name1,name2)
-
-  #merge with ref file
-  ref <- full_join(ref,geno,by=c("marker"="marker"))
-  return(ref)
-}
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/9E3EC0FD-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/9E3EC0FD-contents
deleted file mode 100644
index 902e04361e27306cd36fac0de688e5a6ab80da2c..0000000000000000000000000000000000000000
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/9E3EC0FD-contents
+++ /dev/null
@@ -1,13 +0,0 @@
-# Generated by roxygen2: do not edit by hand
-
-export(geno_strains)
-export(mark_allele)
-export(mark_match)
-export(mark_poly)
-export(mark_prop)
-export(tab_mark)
-export(write_rqtl)
-import(dplyr)
-import(stringr)
-import(tidyr)
-import(utils)
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/C2CE7FEA-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/C2CE7FEA-contents
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/C6286151-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/C6286151-contents
deleted file mode 100644
index 0035346d6c1f1b76d77d1af4868a3329f2545064..0000000000000000000000000000000000000000
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/C6286151-contents
+++ /dev/null
@@ -1,56 +0,0 @@
-## ---- include = FALSE---------------------------------------------------------
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-
-## ----setup--------------------------------------------------------------------
-library(dplyr)
-library(stuart)
-
-## ----annot--------------------------------------------------------------------
-annot_mini <- read.csv(url("https://raw.githubusercontent.com/kbroman/MUGAarrays/master/UWisc/mini_uwisc_v2.csv"))
-
-## ----load---------------------------------------------------------------------
-data(genos)
-summary(genos)
-data(phenos)
-summary(phenos)
-
-## ----strains------------------------------------------------------------------
-strains <- geno_strains(ref=annot_mini,geno=genos,par1=c("StrainsA_1","StrainsA_2"),par2=c("StrainsB_1","StrainsB_2"),name1="parent1",name2="parent2")
-head(strains)
-
-## ----no_parent----------------------------------------------------------------
-genos <- genos %>% filter(!Sample.ID %in% c("StrainsA_1", "StrainsA_2", "StrainsB_1","StrainsB_2"))
-
-## ----tab_mark-----------------------------------------------------------------
-data(stuart_tab)
-summary(stuart_tab)
-
-## ----mark_match---------------------------------------------------------------
-tab2 <- mark_match(stuart_tab,ref=strains)
-
-
-tab2 %>% filter(exclude_match==1)
-
-## ----mark_poly ex-------------------------------------------------------------
-tab2 <- mark_poly(tab2)
-head(tab2)
-
-## ----mark_prop ex-------------------------------------------------------------
-tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
-head(tab2)
-
-## ----mark_allele--------------------------------------------------------------
-tab2 <- mark_allele(tab=tab2,ref=strains,par1="parent1",par2="parent2")
-tab2 %>% arrange(desc(exclude_allele)) %>% head()
-
-## ----mark_allele-strains------------------------------------------------------
-strains %>% filter(marker %in% c("gJAX00038569","gJAX00425031","gUNC12245354","gUNC15530876","gUNC21555204","gUNC21596600")) %>% arrange(marker) %>% select(marker,parent1,parent2)
-
-## ----write_qtl----------------------------------------------------------------
-rqtl_file <- write_rqtl(geno=genos,pheno=phenos,tab=tab2,ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox")
-
-rqtl_file[1:10,1:7]
-
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/D49EE59C-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/D49EE59C-contents
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/E7584E4F-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/E7584E4F-contents
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/lock_file b/.Rproj.user/9DAE6990/sources/s-39B546A6/lock_file
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
index 7779f200af63a93c07e730a2f2b07fa1992b2f1b..f483eb75abcdd04b22b3d1914633421f51c4345f 100644
--- a/.Rproj.user/shared/notebooks/paths
+++ b/.Rproj.user/shared/notebooks/paths
@@ -1,6 +1 @@
-/Users/mariebourdon/stuart_package/stuart/NAMESPACE="6A276B5"
-/Users/mariebourdon/stuart_package/stuart/R/geno_strains.R="1F9B28F5"
-/Users/mariebourdon/stuart_package/stuart/R/genos-data.R="9943E26B"
-/Users/mariebourdon/stuart_package/stuart/R/tab_mark.R="DEC9867F"
-/Users/mariebourdon/stuart_package/stuart/doc/stuaRt.R="E6241391"
-/Users/mariebourdon/stuart_package/stuart/vignettes/stuaRt.Rmd="4D49CCFD"
+/Users/mariebourdon/Documents/PhD/stuart_R/stuart/vignettes/stuaRt.Rmd="C3675061"
diff --git a/R/mark_prop.R b/R/mark_prop.R
index a0827e8c27b02c9d65a6cc3af34cf595f50a5840..8af6e843dc7d88ac3724cf1c46fde5ba9b43f416 100755
--- a/R/mark_prop.R
+++ b/R/mark_prop.R
@@ -14,6 +14,7 @@
 
 #### 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){
   #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))