diff --git a/.Rd2pdf36888/Rd2.tex b/.Rd2pdf36888/Rd2.tex
new file mode 100644
index 0000000000000000000000000000000000000000..6827864d91a244019dffa6de1df989552ec11cf0
--- /dev/null
+++ b/.Rd2pdf36888/Rd2.tex
@@ -0,0 +1,12 @@
+\documentclass[letterpaper]{book}
+\usepackage[times,inconsolata,hyper]{Rd}
+\usepackage{makeidx}
+\usepackage[latin1]{inputenc} % @SET ENCODING@
+% \usepackage{graphicx} % @USE GRAPHICX@
+\makeindex{}
+\begin{document}
+\chapter*{}
+\begin{center}
+{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of \file{stuart}}}
+\par\bigskip{\large \today}
+\end{center}
diff --git a/.Rd2pdf36909/Rd2.tex b/.Rd2pdf36909/Rd2.tex
new file mode 100644
index 0000000000000000000000000000000000000000..6ed07fce277330c646f980fb54b162b7f1a1b238
--- /dev/null
+++ b/.Rd2pdf36909/Rd2.tex
@@ -0,0 +1,12 @@
+\documentclass[letterpaper]{book}
+\usepackage[times,inconsolata,hyper]{Rd}
+\usepackage{makeidx}
+\usepackage[latin1]{inputenc} % @SET ENCODING@
+% \usepackage{graphicx} % @USE GRAPHICX@
+\makeindex{}
+\begin{document}
+\chapter*{}
+\begin{center}
+{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of \file{stuaRt}}}
+\par\bigskip{\large \today}
+\end{center}
diff --git a/.Rhistory b/.Rhistory
index 84a1385b297f884c6ed7ed38dfa8256d40b530ba..5bb5b6edfd0467a2548107e48d9335f20e7bf051 100644
--- a/.Rhistory
+++ b/.Rhistory
@@ -1,19 +1,3 @@
-# #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 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")
-# }
-# #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))
-# tab <- tab %>% select(-c(p_HM1,p_HM2,p_HT,p_NA,n_geno))
-# return(tab)
}
test_tab <- tab2[1:20,]
tab3 <- mark_prop(test_tab,cross="F2",pval=0.05)
@@ -510,3 +494,19 @@ devtools::build_vignettes()
devtools::build_vignettes()
devtools::build_vignettes()
devtools::build_vignettes()
+demo()
+install.packages("devtools")
+install.packages("usethat")
+install.packages("raportools")
+install.packages("rapportools")
+install.packages("roxygen2")
+install.packages("testthat")
+library(stuart)
+library(dplyr)
+library(stuart)
+knitr::opts_chunk$set(
+collapse = TRUE,
+comment = "#>"
+)
+library(dplyr)
+library(stuart)
diff --git a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/9DAE69902F7E98B0/chunks.json b/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/9DAE69902F7E98B0/chunks.json
deleted file mode 100644
index 2ae2af1a405c387b16b410517bf321515a703b7b..0000000000000000000000000000000000000000
--- a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/9DAE69902F7E98B0/chunks.json
+++ /dev/null
@@ -1 +0,0 @@
-{"chunk_definitions":[{"chunk_id":"csetup_chunk","chunk_label":"setup","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","include":false,"label":"setup"},"row":31,"row_count":1,"visible":true},{"chunk_id":"cvrfzlkmsnd5m","chunk_label":"annot","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"annot"},"row":45,"row_count":1,"visible":true},{"chunk_id":"c0s26bf1pu5ys","chunk_label":"load","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"load"},"row":60,"row_count":1,"visible":true},{"chunk_id":"cxuyx1brxodqv","chunk_label":"strains","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"strains"},"row":73,"row_count":1,"visible":true},{"chunk_id":"ccbr8kr5rmfiz","chunk_label":"no_parent","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"no_parent"},"row":78,"row_count":1,"visible":true},{"chunk_id":"ceekbogybpgbx","chunk_label":"tab_mark","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"tab_mark"},"row":91,"row_count":1,"visible":true},{"chunk_id":"cgfik6q17v45t","chunk_label":"mark_match","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"mark_match"},"row":100,"row_count":1,"visible":true},{"chunk_id":"c4gkr1xb8o1a9","chunk_label":"mark_poly ex","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"mark_poly ex"},"row":109,"row_count":1,"visible":true},{"chunk_id":"cp87d27x07m61","chunk_label":"mark_prop ex","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"mark_prop ex"},"row":186,"row_count":1,"visible":true}],"default_chunk_options":{},"doc_write_time":1623065923,"working_dir":null}
\ No newline at end of file
diff --git a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/9DAE6990E3DC937A/chunks.json b/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/9DAE6990E3DC937A/chunks.json
deleted file mode 100644
index 93244d6d228956f362c92c72b489998013de4fe4..0000000000000000000000000000000000000000
--- a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/9DAE6990E3DC937A/chunks.json
+++ /dev/null
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\ No newline at end of file
diff --git a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/9DAE6990E6946356/chunks.json b/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/9DAE6990E6946356/chunks.json
deleted file mode 100644
index 49caf2049d6ca5e813dae2a5c56e8e5c8613efde..0000000000000000000000000000000000000000
--- a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/9DAE6990E6946356/chunks.json
+++ /dev/null
@@ -1 +0,0 @@
-{"chunk_definitions":[{"chunk_id":"culdjhv7njxmo","chunk_label":"unnamed-chunk-1","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","include":false,"label":"unnamed-chunk-3"},"row":15,"row_count":1,"visible":true},{"chunk_id":"csetup_chunk","chunk_label":"setup","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","include":false,"label":"setup"},"row":31,"row_count":1,"visible":true},{"chunk_id":"cvrfzlkmsnd5m","chunk_label":"annot","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"annot"},"row":45,"row_count":1,"visible":true},{"chunk_id":"c0s26bf1pu5ys","chunk_label":"load","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"load"},"row":60,"row_count":1,"visible":true},{"chunk_id":"cxuyx1brxodqv","chunk_label":"strains","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"strains"},"row":73,"row_count":1,"visible":true},{"chunk_id":"ccbr8kr5rmfiz","chunk_label":"no_parent","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"no_parent"},"row":78,"row_count":1,"visible":true},{"chunk_id":"ceekbogybpgbx","chunk_label":"tab_mark","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"tab_mark"},"row":91,"row_count":1,"visible":true},{"chunk_id":"cgfik6q17v45t","chunk_label":"mark_match","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"mark_match"},"row":100,"row_count":1,"visible":true},{"chunk_id":"c4gkr1xb8o1a9","chunk_label":"mark_poly ex","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"mark_poly ex"},"row":109,"row_count":1,"visible":true},{"chunk_id":"cp87d27x07m61","chunk_label":"mark_prop ex","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","label":"mark_prop ex"},"row":116,"row_count":1,"visible":true}],"default_chunk_options":{},"doc_write_time":1623085296,"working_dir":null}
\ No newline at end of file
diff --git a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/chunks.json b/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/chunks.json
deleted file mode 100644
index 93244d6d228956f362c92c72b489998013de4fe4..0000000000000000000000000000000000000000
--- a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/chunks.json
+++ /dev/null
@@ -1 +0,0 @@
-{"chunk_definitions":[{"chunk_id":"culdjhv7njxmo","chunk_label":"unnamed-chunk-1","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","include":false,"label":"unnamed-chunk-1"},"row":15,"row_count":1,"visible":true},{"chunk_id":"csetup_chunk","chunk_label":"setup","document_id":"96AB3736","expansion_state":0,"options":{"engine":"r","include":false,"label":"setup"},"row":31,"row_count":1,"visible":true}],"doc_write_time":1623691782}
\ No newline at end of file
diff --git a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/csetup_chunk/000002.csv b/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/csetup_chunk/000002.csv
deleted file mode 100644
index 1ef951207dd446f19eef7d86d5c04fabdac7504d..0000000000000000000000000000000000000000
--- a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/csetup_chunk/000002.csv
+++ /dev/null
@@ -1,16 +0,0 @@
-"0","library(dplyr)"
-"2","
-Attachement du package : ‘dplyr’
-
-"
-"2","The following objects are masked from ‘package:stats’:
-
- filter, lag
-
-"
-"2","The following objects are masked from ‘package:base’:
-
- intersect, setdiff, setequal, union
-
-"
-"0","library(stuart)"
diff --git a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/culdjhv7njxmo/000002.csv b/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/culdjhv7njxmo/000002.csv
deleted file mode 100644
index 56c8fe6a2ad810a56b647940468c76816c70636f..0000000000000000000000000000000000000000
--- a/.Rproj.user/shared/notebooks/C3675061-stuaRt/1/s/culdjhv7njxmo/000002.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-"0","knitr::opts_chunk$set("
-"0"," collapse = TRUE,"
-"0"," comment = ""#>"""
-"0",")"
diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
index 62c82257f26e5e04a3f11cee7e7a3fb047f5f1c6..8274802bed17cf345bd9ae5194f830b2d0379fe6 100644
--- a/.Rproj.user/shared/notebooks/paths
+++ b/.Rproj.user/shared/notebooks/paths
@@ -1,2 +1,5 @@
-/Users/mariebourdon/Documents/PhD/stuart_R/stuart/vignettes/stuaRt.Rmd="C3675061"
-/Users/mariebourdon/stuart_package/stuart_old/R/mark_prop.R="5087875"
+/home/marie/Documents/stuart_package/stuart/R/mark_prop.R="19C6446D"
+/home/marie/Documents/stuart_package/stuart/R/write_rqtl.R="D25FAC55"
+/home/marie/Documents/stuart_package/stuart/README.Rmd="C395B1B3"
+/home/marie/Documents/stuart_package/stuart/README.md="8BBA9900"
+/home/marie/Documents/stuart_package/stuart/vignettes/stuaRt.Rmd="007031F6"
diff --git a/.gitignore b/.gitignore
index 00b31dc8122796441fafc7815eb71f44411a5dd5..1b5a6ad69a3f785b27b1cb0794b69619bfabc1a4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,5 @@
doc
Meta
+.Rproj.user
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
index 911e98e77fb0cf49335cbfd32c13ed959635aace..ed771c3309f4688acb8068a38b51ed44551a7581 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: stuart
Title: stuart
-Version: 1.0.0
+Version: 1.0.2
Authors@R:
person(given = "Marie",
family = "Bourdon",
diff --git a/R/genos-data.R b/R/genos-data.R
index fd50eb0ea6a1188c1f619aa7510b6b276c9c2895..55ceabf71141f7b93b88bc573a8c66e86642a0fc 100755
--- a/R/genos-data.R
+++ b/R/genos-data.R
@@ -1,8 +1,8 @@
#' Data frame with miniMUGA genotyping of F2 individuals and parental strains
#'
-#' A dataset containing the genotypes of 176 F2 individuals
+#' A dataset containing the genotypes of 176 F2 individuals and 4 individuals of 2 laboratory strains
#'
-#' @format A data frame with 2002493 observations of 11 variables
+#' @format A data frame with 1957993 observations of 11 variables
"genos"
diff --git a/R/mark_allele.R b/R/mark_allele.R
index f83d3ac4ea31d973b58101efc2b7f0862fb8714a..1646ed5b30ec06af760e4cc03ae537448fb46770 100755
--- a/R/mark_allele.R
+++ b/R/mark_allele.R
@@ -10,7 +10,7 @@
#'
#' @export
#'
-mark_allele <- function(tab,ref,par1,par2){
+mark_allele <- function(tab,ref,par1,par2,parNH=TRUE){
#markers of ref df as characters
ref$marker <- as.character(ref$marker)
@@ -24,8 +24,11 @@ mark_allele <- function(tab,ref,par1,par2){
ref <- ref %>% select(marker,!!sym(par1),!!sym(par2))
tab <- full_join(tab,ref,by=c("marker"="marker"))
+ print(parNH)
#function core
- tab <- tab %>% mutate(exclude_allele = case_when(is.na(allele_2)==FALSE &
+ tab <- tab %>% mutate(exclude_allele = case_when(parNH==FALSE &
+ (!!sym(par1) == "N" | !!sym(par2) == "N" | !!sym(par1) == "H" | !!sym(par2) == "H") ~ 1,
+ is.na(allele_2)==FALSE &
!!sym(par1) != "N" & !!sym(par2) != "N" & !!sym(par1) != "H" & !!sym(par2) != "H" &
((allele_1!=!!sym(par1) & allele_1!=!!sym(par2)) | (allele_2!=!!sym(par1) & allele_2!=!!sym(par2))) ~ 1,
is.na(allele_2)==FALSE &
@@ -40,6 +43,8 @@ mark_allele <- function(tab,ref,par1,par2){
T ~ 0)
)
+ print(tab)
+
tab <- tab %>% select(-c(!!sym(par1),!!sym(par2)))
return(tab)
diff --git a/R/mark_prop.R b/R/mark_prop.R
index 9b64227c7609b19b93b4f2e23a78be0710971df7..499ed92b1ca36c27647d2e77a5ec14b0195be7ec 100755
--- a/R/mark_prop.R
+++ b/R/mark_prop.R
@@ -1,6 +1,6 @@
#' @title Exclude markers depending on proportions of homo/hetorozygous
#'
-#' @description uses the dataframe produced by the tab_mark function and fills the "exclude" column for all the markers that present odd proportions of each genotype. You can define these proportions thanks to the arguments of the function.
+#' @description This function uses the dataframe produced by the tab_mark function and fills the "exclude" column for all the markers that present odd proportions of each genotype. You can define these proportions thanks to the arguments of the function.
#' @param tab data frame obtained with tab_mark function.
#' @param cross F2 or N2.
#' @param homo proportion of homozygous individuals under which the marker is excluded. Will apply on both homozygous genotypes for a F2, but only on one for N2.
@@ -15,17 +15,12 @@
#### mark_prop ####
## excludes markers depending on proportions of homo/hetorozygous
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 = (n_HM1 + n_HM2 + n_HT))
-
- #calculate proportion of each genotype
- tab <- tab %>% mutate(p_HM1 = n_HM1/n_geno)
- tab <- tab %>% mutate(p_HM2 = n_HM2/n_geno)
- 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)
+ print(names)
+
+ #calculate total number of individuals genotyped for each marker
+ tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
#stop if cross != "F2" or "N2"
@@ -41,12 +36,21 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
#stop with prop of na
+ #calculate proportion
+ tab <- tab %>% mutate(p_NA = n_NA/(n_geno+n_NA))
+
tab <- tab %>%
mutate(exclude_prop=case_when(p_NA > na ~ 1,
T ~ 0))
- #stop with prop of homo/hetero
+ #exclude with prop of homo/hetero
if(is.na(pval)==TRUE){
+ #calculate proportion of each genotype
+ tab <- tab %>% mutate(p_HM1 = n_HM1/n_geno)
+ tab <- tab %>% mutate(p_HM2 = n_HM2/n_geno)
+ tab <- tab %>% mutate(p_HT = n_HT/n_geno)
+
+
tab <- tab %>%
mutate(exclude_prop=case_when(p_NA > na ~ 1,
cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
@@ -55,19 +59,19 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
))
}
- #stop with pval chisq.test
+ #exclude 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)
+ full_join(.,tab,by=all_of(names))
tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
T ~ exclude_prop))
}
-
- tab <- tab %>% select(names)
- return(tab)
+ print(tab)
+ tab <- tab %>% select(all_of(names),exclude_prop)
+ print(tab)
}
diff --git a/R/write_rqtl.R b/R/write_rqtl.R
index ff77d827447e2bc92cc0f7a60c317db946a7e179..f682977db1d797c74d32a3b102b5a48a2c2f2341 100755
--- a/R/write_rqtl.R
+++ b/R/write_rqtl.R
@@ -20,7 +20,7 @@
#'
#### write_rqtl ####
## write data frame in rqtl format (csv), if path != NA writes the file in the path indicated
-write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
+write_rqtl <- function(geno,pheno,tab,ref,par1,par2,par_N=TRUE,prefix,pos,path=NA){
#rename df columns
geno <- geno %>% rename("marker"=1,
"id"=2,
@@ -95,7 +95,7 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
!!sym(par1)%in%c("H","N") ~ "0",
###homozygous 2
(!!sym(par1)%in%c("H","N") | !!sym(par2)%in%c("H","N")) &
- !!sym(par2)%in%c("H","N") ~ "2",
+ !!sym(par2)%in%c("H","N") ~ "2"
)
)
diff --git a/README.Rmd b/README.Rmd
index 3312c8ecc269c9d6b709d556661415cb41627995..9084c932364230c0b6b73240cfd9ace90e5fe627 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -22,11 +22,19 @@ stuart is a R package used to analyze whole genome genotyping results of animals
## Installation
-You can install the released version of stuart from GitLab
+You can install the released version of stuart from GitLab, by dowloading the latest tar.gz file and installing it with:
-``` r
+```{r}
+install.packages(path_to/stuart_X.Y.Z.tar.gz, repos = NULL, type="source")
```
+
+Or directly in R with:
+```{r}
+devtools::install_gitlab(repo="mouselab/stuart",host="gitlab.pasteur.fr")
+```
+
+
## Example
To see an example of the use of stuart package with miniMUGA array, consult the package vignette.
diff --git a/man/genos.Rd b/man/genos.Rd
index 1aad5938b7e0d7fd09e31b1ca35a07c887f09449..d301eb61019491d49f52adb192758e3cba5c00e8 100755
--- a/man/genos.Rd
+++ b/man/genos.Rd
@@ -5,12 +5,12 @@
\alias{genos}
\title{Data frame with miniMUGA genotyping of F2 individuals and parental strains}
\format{
-A data frame with 2002493 observations of 11 variables
+A data frame with 1957993 observations of 11 variables
}
\usage{
genos
}
\description{
-A dataset containing the genotypes of 176 F2 individuals
+A dataset containing the genotypes of 176 F2 individuals and 4 individuals of 2 laboratory strains
}
\keyword{datasets}
diff --git a/man/mark_allele.Rd b/man/mark_allele.Rd
index 6bb2a189321bcc7d4990373d4ff75b65d3950546..c4c1be236ad93741de0e458d5d9cd20bcf1a4885 100755
--- a/man/mark_allele.Rd
+++ b/man/mark_allele.Rd
@@ -4,7 +4,7 @@
\alias{mark_allele}
\title{Exclude markers that have different alleles in the individuals of the cross and in parental strains}
\usage{
-mark_allele(tab, ref, par1, par2)
+mark_allele(tab, ref, par1, par2, parNH = TRUE)
}
\arguments{
\item{tab}{data frame obtained with tab_mark function}
diff --git a/man/mark_prop.Rd b/man/mark_prop.Rd
index fa0163af9fb00460925f56115d4688185f175841..d59da6ffe1752a8c9394d044682e7e0550b79184 100755
--- a/man/mark_prop.Rd
+++ b/man/mark_prop.Rd
@@ -4,7 +4,7 @@
\alias{mark_prop}
\title{Exclude markers depending on proportions of homo/hetorozygous}
\usage{
-mark_prop(tab, cross, homo = NA, hetero = NA, na = 0.5)
+mark_prop(tab, cross, homo = NA, hetero = NA, pval = NA, na = 0.5)
}
\arguments{
\item{tab}{data frame obtained with tab_mark function.}
@@ -18,5 +18,5 @@ mark_prop(tab, cross, homo = NA, hetero = NA, na = 0.5)
\item{na}{proportion of non-genotyped individuals above which the marker is excluded.}
}
\description{
-uses the dataframe produced by the tab_mark function and fills the "exclude" column for all the markers that present odd proportions of each genotype. You can define these proportions thanks to the arguments of the function.
+This function uses the dataframe produced by the tab_mark function and fills the "exclude" column for all the markers that present odd proportions of each genotype. You can define these proportions thanks to the arguments of the function.
}
diff --git a/man/stuart_tab.Rd b/man/stuart_tab.Rd
index ebe357ac22fecfe7fca149db36df30412e4d55ea..aeb4a86eba3e376a24df48ee03fcd7a75c237aaf 100644
--- a/man/stuart_tab.Rd
+++ b/man/stuart_tab.Rd
@@ -7,9 +7,9 @@
\format{
A data frame with 11125 rows and 7 variables
\describe{
-\item{SNP.Name}{name of the marker}
-\item{Allele_1}{first allele of the marker}
-\item{Allele_2}{second allele of the marker}
+\item{marker}{name of the marker}
+\item{allele_1}{first allele of the marker}
+\item{allele_2}{second allele of the marker}
\item{n_HM1}{number of homozygous individuals for the first allele}
\item{n_HM2}{number of homozygous individuals for the second allele}
\item{n_HT}{number of heterozygous individuals}
diff --git a/man/write_rqtl.Rd b/man/write_rqtl.Rd
index 0a52b05dbafb614aa89bd3209a8d3f86d255b50e..0f1280d636698fcdec2c7c512a4fa921f764a668 100755
--- a/man/write_rqtl.Rd
+++ b/man/write_rqtl.Rd
@@ -4,7 +4,18 @@
\alias{write_rqtl}
\title{Create data frame in Rqtl CSV format}
\usage{
-write_rqtl(geno, pheno, tab, ref, par1, par2, prefix, pos, path = NA)
+write_rqtl(
+ geno,
+ pheno,
+ tab,
+ ref,
+ par1,
+ par2,
+ par_N = TRUE,
+ prefix,
+ pos,
+ path = NA
+)
}
\arguments{
\item{geno}{data frame with the genotyping results for your cross}
diff --git a/stuart_1.0.0.tar.gz b/stuart_1.0.0.tar.gz
deleted file mode 100644
index cf42723acb6e9bebdf0f34e0ea947450bbe23ded..0000000000000000000000000000000000000000
Binary files a/stuart_1.0.0.tar.gz and /dev/null differ
diff --git a/stuart_1.0.0.pdf b/stuart_1.0.2.pdf
similarity index 53%
rename from stuart_1.0.0.pdf
rename to stuart_1.0.2.pdf
index d5c0dc7e08fd43905d9bbf83133afb2dcf72ca46..ba8a6d728314b0933827e229787f7b8d912ac958 100644
Binary files a/stuart_1.0.0.pdf and b/stuart_1.0.2.pdf differ
diff --git a/stuart_1.0.2.tar.gz b/stuart_1.0.2.tar.gz
new file mode 100644
index 0000000000000000000000000000000000000000..e19e5f3982702b23d735577bbea8eda15ecceaee
Binary files /dev/null and b/stuart_1.0.2.tar.gz differ
diff --git a/vignettes/stuaRt.Rmd b/vignettes/stuaRt.Rmd
index 0359797b0e482cb2609d087403374f6b007ed5bc..b4af84f39711829855378cf4d6021838f3cc450f 100755
--- a/vignettes/stuaRt.Rmd
+++ b/vignettes/stuaRt.Rmd
@@ -95,8 +95,6 @@ Then we will use the different mark_* functions in order to filter the markers.
```{r mark_match}
tab2 <- mark_match(stuart_tab,ref=strains)
-
-
tab2 %>% filter(exclude_match==1)
```