diff --git a/.Rproj.user/9DAE6990/sources/prop/5B8691C7 b/.Rproj.user/9DAE6990/sources/prop/5B8691C7
index 1f3aca9005e6c2bfeb0a9b999c80078a7d57fb23..dd976e56d512c526a7b5d85f156ef0835b1871df 100644
--- a/.Rproj.user/9DAE6990/sources/prop/5B8691C7
+++ b/.Rproj.user/9DAE6990/sources/prop/5B8691C7
@@ -1,4 +1,4 @@
{
- "cursorPosition" : "48,32",
- "scrollLine" : "33"
+ "cursorPosition" : "84,18",
+ "scrollLine" : "94"
}
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diff --git a/.Rproj.user/9DAE6990/sources/prop/65312719 b/.Rproj.user/9DAE6990/sources/prop/65312719
new file mode 100644
index 0000000000000000000000000000000000000000..7a73a41bfdf76d6f793007240d80983a52f15f97
--- /dev/null
+++ b/.Rproj.user/9DAE6990/sources/prop/65312719
@@ -0,0 +1,2 @@
+{
+}
\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/sources/prop/D602FFE4 b/.Rproj.user/9DAE6990/sources/prop/D602FFE4
index 082b02e9e6bf90cc948fb06aced67605250d702c..59518e3e3c0da54f662f7dd699fd976f910ca7c7 100644
--- a/.Rproj.user/9DAE6990/sources/prop/D602FFE4
+++ b/.Rproj.user/9DAE6990/sources/prop/D602FFE4
@@ -1,5 +1,5 @@
{
- "cursorPosition" : "127,25",
+ "cursorPosition" : "135,15",
"last_setup_crc32" : "39B546A65bfca283",
- "scrollLine" : "119"
+ "scrollLine" : "130"
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\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/sources/prop/INDEX b/.Rproj.user/9DAE6990/sources/prop/INDEX
index b5e12590bd67d9b3c876796a41d7a702c54e6a41..16f98885be4bba0b41bed600c49af1738abd995d 100644
--- a/.Rproj.user/9DAE6990/sources/prop/INDEX
+++ b/.Rproj.user/9DAE6990/sources/prop/INDEX
@@ -9,5 +9,6 @@
~%2Fstuart_package%2Fstuart%2FR%2Fstuart_tab-data.R="7411866"
~%2Fstuart_package%2Fstuart%2FR%2Ftab_mark.R="7FA3B215"
~%2Fstuart_package%2Fstuart%2FR%2Fwrite_rqtl.R="5B8691C7"
+~%2Fstuart_package%2Fstuart%2Fdoc%2FstuaRt.R="65312719"
~%2Fstuart_package%2Fstuart%2Fvignettes%2FstuaRt.R="EBD625D2"
~%2Fstuart_package%2Fstuart%2Fvignettes%2FstuaRt.Rmd="D602FFE4"
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58 b/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58
index 7b1630989ded63aeb84eee2ab57468fa86e768a2..f68fb4c1e8cf5d5be740afb5ed88aef0a4f0d0a3 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58
+++ b/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58
@@ -5,15 +5,15 @@
"dirty" : false,
"encoding" : "UTF-8",
"folds" : "",
- "hash" : "3120719904",
+ "hash" : "1139135974",
"id" : "45D91D58",
- "lastKnownWriteTime" : 1622621980,
- "last_content_update" : 1622621980790,
+ "lastKnownWriteTime" : 1622648301,
+ "last_content_update" : 1622648301329,
"path" : "~/stuart_package/stuart/R/write_rqtl.R",
"project_path" : "R/write_rqtl.R",
"properties" : {
- "cursorPosition" : "48,32",
- "scrollLine" : "33"
+ "cursorPosition" : "84,18",
+ "scrollLine" : "94"
},
"read_only" : false,
"read_only_alternatives" : [
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58-contents
index cbfc05505af72a38887f69cdef97707b5d8e8bf1..0926c5c3a44d009a46244ee5d52835afb1309978 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58-contents
+++ b/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58-contents
@@ -21,6 +21,12 @@
#### 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){
+ #rename df columns
+ geno <- geno %>% rename("marker"=1,
+ "id"=2,
+ "allele_1"=3,
+ "allele_2"=4)
+
#extract snps non excluded
if("exclude_match" %in% colnames(tab)){
tab <- tab %>% filter(exclude_match==0)
@@ -40,7 +46,7 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
#filter genotypes for non excluded markers in geno file
- geno <- geno %>% select(c(SNP.Name,Sample.ID,Allele1...Forward,Allele2...Forward)) %>% filter(SNP.Name %in% tab$SNP.Name)
+ geno <- geno %>% select(c(marker,id,allele_1,allele_2)) %>% filter(marker %in% tab$marker)
#recode parents' names to match column names nomenclature
par1 <- make.names(par1)
@@ -51,33 +57,33 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
ref <- ref %>% select(marker,chr,!!sym(pos),!!sym(par1),!!sym(par2))
#merge genotypes with parents
- geno <- left_join(geno,ref,by=c("SNP.Name"="marker"))
+ geno <- left_join(geno,ref,by=c("marker"="marker"))
#recode "-" in "N" in geno file
- geno <- geno %>% mutate(Allele1...Forward = recode(Allele1...Forward,
+ geno <- geno %>% mutate(allele_1 = recode(allele_1,
"-" = "N"))
- geno <- geno %>% mutate(Allele2...Forward = recode(Allele2...Forward,
+ geno <- geno %>% mutate(allele_2 = recode(allele_2,
"-" = "N"))
#recode geno in factors with same levels
- geno <- geno %>% mutate(Allele1...Forward = factor(Allele1...Forward,levels=c("A","C","G","H","N","T")))
- geno <- geno %>% mutate(Allele2...Forward = factor(Allele2...Forward,levels=c("A","C","G","H","N","T")))
+ geno <- geno %>% mutate(allele_1 = factor(allele_1,levels=c("A","C","G","H","N","T")))
+ geno <- geno %>% mutate(allele_2 = factor(allele_2,levels=c("A","C","G","H","N","T")))
#recode genotypes depending on parents' genotypes
geno <- geno %>% mutate(Geno = case_when(
#if one allele not genotyped:
- Allele1...Forward=="N" | Allele2...Forward=="N" ~ "NA",
+ allele_1=="N" | allele_2=="N" ~ "NA",
#if both alleles genotyped
##homozygous 0
- Allele1...Forward==Allele2...Forward & Allele1...Forward==!!sym(par1) ~ "0",
+ allele_1==allele_2 & allele_1==!!sym(par1) ~ "0",
##homozygous 2
- Allele1...Forward==Allele2...Forward & Allele1...Forward==!!sym(par2) ~ "2",
+ allele_1==allele_2 & allele_1==!!sym(par2) ~ "2",
##heterozygous
- Allele1...Forward!=Allele2...Forward ~ "1",
+ allele_1!=allele_2 ~ "1",
#if parental strains are N/H
##homozygous for parent that is N/H
@@ -92,33 +98,33 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
#keep positions of markers
- markers <- geno %>% select(SNP.Name,chr,!!sym(pos)) %>% distinct()
+ markers <- geno %>% select(marker,chr,!!sym(pos)) %>% distinct()
markers <- markers %>% arrange(chr,!!sym(pos))
#keep only interesting columns in geno file
geno <- geno %>% arrange(chr,!!sym(pos))
- geno <- geno %>% select(SNP.Name,Sample.ID,Geno)
+ geno <- geno %>% select(marker,id,Geno)
#remove prefix
- geno <- geno %>% mutate(Sample.ID=str_remove(Sample.ID,prefix))
+ geno <- geno %>% mutate(id=str_remove(id,prefix))
#keep only non excluded markers and merge with positions
- markers <- markers %>% mutate(SNP.Name=as.character(SNP.Name))
+ markers <- markers %>% mutate(marker=as.character(marker))
markers <- markers %>% mutate(chr=as.character(chr))
- geno <- markers %>% select(SNP.Name,chr,!!sym(pos)) %>% full_join(.,geno,by="SNP.Name")
+ geno <- markers %>% select(marker,chr,!!sym(pos)) %>% full_join(.,geno,by="marker")
#pivoting
- geno <- geno %>% pivot_wider(names_from = c(SNP.Name,chr,!!sym(pos)),values_from = Geno,names_sep=",")
- geno <- geno %>% mutate(Sample.ID=as.character(Sample.ID))
- geno <- geno %>% rename("Sample.ID,,"=Sample.ID)
+ geno <- geno %>% pivot_wider(names_from = c(marker,chr,!!sym(pos)),values_from = Geno,names_sep=",")
+ geno <- geno %>% mutate(id=as.character(id))
+ geno <- geno %>% rename("id,,"=id)
#merge with phenotype file
pheno <- pheno %>% mutate_all(as.character)
colnames(pheno) <- str_c(colnames(pheno),",,")
- qtl_file <- right_join(pheno,geno,by=c("Ind,,"="Sample.ID,,"))
+ qtl_file <- right_join(pheno,geno,by=c("Ind,,"="id,,"))
#prepare file
qtl_file <- rbind(colnames(qtl_file),qtl_file)
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736 b/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736
index bf870f4dc334ee3de6a448d1ad982d8d44936526..ff216ba631ada3582dc5f0c3069563828d2cae4a 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736
+++ b/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736
@@ -5,16 +5,16 @@
"dirty" : false,
"encoding" : "UTF-8",
"folds" : "",
- "hash" : "3134659970",
+ "hash" : "2014255563",
"id" : "96AB3736",
- "lastKnownWriteTime" : 1622647884,
- "last_content_update" : 1622647884538,
+ "lastKnownWriteTime" : 1622648726,
+ "last_content_update" : 1622648726992,
"path" : "~/stuart_package/stuart/vignettes/stuaRt.Rmd",
"project_path" : "vignettes/stuaRt.Rmd",
"properties" : {
- "cursorPosition" : "127,25",
+ "cursorPosition" : "135,15",
"last_setup_crc32" : "39B546A65bfca283",
- "scrollLine" : "119"
+ "scrollLine" : "130"
},
"read_only" : false,
"read_only_alternatives" : [
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736-contents
index 2dfb70edac53e76fd1e666150ea7dd15d9442f65..e73872a8f734ba8177b36fc84e013586614d4848 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736-contents
+++ b/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736-contents
@@ -133,7 +133,7 @@ strains %>% filter(marker %in% c("gJAX00038569","gJAX00425031","gUNC12245354","g
After excluding the problematic markers, we can create the R/qtl file. The individuals must have the same ID in the geno and in the pheno file. If there is a prefix in the geno file that must be removed in order to acheive this, you can use the "prefix" argument. The "path" argument can be used in order to create a CSV file that you can laod with `qtl::read.cross`.
-```{r write_qtl,eval=F}
+```{r 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/C6286151-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/C6286151-contents
new file mode 100644
index 0000000000000000000000000000000000000000..0035346d6c1f1b76d77d1af4868a3329f2545064
--- /dev/null
+++ b/.Rproj.user/9DAE6990/sources/s-39B546A6/C6286151-contents
@@ -0,0 +1,56 @@
+## ---- 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/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
index 987226a929aa70c98c5954e2e9f8ce2716ea30d6..7779f200af63a93c07e730a2f2b07fa1992b2f1b 100644
--- a/.Rproj.user/shared/notebooks/paths
+++ b/.Rproj.user/shared/notebooks/paths
@@ -2,4 +2,5 @@
/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"
diff --git a/R/write_rqtl.R b/R/write_rqtl.R
index cbfc05505af72a38887f69cdef97707b5d8e8bf1..0926c5c3a44d009a46244ee5d52835afb1309978 100755
--- a/R/write_rqtl.R
+++ b/R/write_rqtl.R
@@ -21,6 +21,12 @@
#### 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){
+ #rename df columns
+ geno <- geno %>% rename("marker"=1,
+ "id"=2,
+ "allele_1"=3,
+ "allele_2"=4)
+
#extract snps non excluded
if("exclude_match" %in% colnames(tab)){
tab <- tab %>% filter(exclude_match==0)
@@ -40,7 +46,7 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
#filter genotypes for non excluded markers in geno file
- geno <- geno %>% select(c(SNP.Name,Sample.ID,Allele1...Forward,Allele2...Forward)) %>% filter(SNP.Name %in% tab$SNP.Name)
+ geno <- geno %>% select(c(marker,id,allele_1,allele_2)) %>% filter(marker %in% tab$marker)
#recode parents' names to match column names nomenclature
par1 <- make.names(par1)
@@ -51,33 +57,33 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
ref <- ref %>% select(marker,chr,!!sym(pos),!!sym(par1),!!sym(par2))
#merge genotypes with parents
- geno <- left_join(geno,ref,by=c("SNP.Name"="marker"))
+ geno <- left_join(geno,ref,by=c("marker"="marker"))
#recode "-" in "N" in geno file
- geno <- geno %>% mutate(Allele1...Forward = recode(Allele1...Forward,
+ geno <- geno %>% mutate(allele_1 = recode(allele_1,
"-" = "N"))
- geno <- geno %>% mutate(Allele2...Forward = recode(Allele2...Forward,
+ geno <- geno %>% mutate(allele_2 = recode(allele_2,
"-" = "N"))
#recode geno in factors with same levels
- geno <- geno %>% mutate(Allele1...Forward = factor(Allele1...Forward,levels=c("A","C","G","H","N","T")))
- geno <- geno %>% mutate(Allele2...Forward = factor(Allele2...Forward,levels=c("A","C","G","H","N","T")))
+ geno <- geno %>% mutate(allele_1 = factor(allele_1,levels=c("A","C","G","H","N","T")))
+ geno <- geno %>% mutate(allele_2 = factor(allele_2,levels=c("A","C","G","H","N","T")))
#recode genotypes depending on parents' genotypes
geno <- geno %>% mutate(Geno = case_when(
#if one allele not genotyped:
- Allele1...Forward=="N" | Allele2...Forward=="N" ~ "NA",
+ allele_1=="N" | allele_2=="N" ~ "NA",
#if both alleles genotyped
##homozygous 0
- Allele1...Forward==Allele2...Forward & Allele1...Forward==!!sym(par1) ~ "0",
+ allele_1==allele_2 & allele_1==!!sym(par1) ~ "0",
##homozygous 2
- Allele1...Forward==Allele2...Forward & Allele1...Forward==!!sym(par2) ~ "2",
+ allele_1==allele_2 & allele_1==!!sym(par2) ~ "2",
##heterozygous
- Allele1...Forward!=Allele2...Forward ~ "1",
+ allele_1!=allele_2 ~ "1",
#if parental strains are N/H
##homozygous for parent that is N/H
@@ -92,33 +98,33 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
#keep positions of markers
- markers <- geno %>% select(SNP.Name,chr,!!sym(pos)) %>% distinct()
+ markers <- geno %>% select(marker,chr,!!sym(pos)) %>% distinct()
markers <- markers %>% arrange(chr,!!sym(pos))
#keep only interesting columns in geno file
geno <- geno %>% arrange(chr,!!sym(pos))
- geno <- geno %>% select(SNP.Name,Sample.ID,Geno)
+ geno <- geno %>% select(marker,id,Geno)
#remove prefix
- geno <- geno %>% mutate(Sample.ID=str_remove(Sample.ID,prefix))
+ geno <- geno %>% mutate(id=str_remove(id,prefix))
#keep only non excluded markers and merge with positions
- markers <- markers %>% mutate(SNP.Name=as.character(SNP.Name))
+ markers <- markers %>% mutate(marker=as.character(marker))
markers <- markers %>% mutate(chr=as.character(chr))
- geno <- markers %>% select(SNP.Name,chr,!!sym(pos)) %>% full_join(.,geno,by="SNP.Name")
+ geno <- markers %>% select(marker,chr,!!sym(pos)) %>% full_join(.,geno,by="marker")
#pivoting
- geno <- geno %>% pivot_wider(names_from = c(SNP.Name,chr,!!sym(pos)),values_from = Geno,names_sep=",")
- geno <- geno %>% mutate(Sample.ID=as.character(Sample.ID))
- geno <- geno %>% rename("Sample.ID,,"=Sample.ID)
+ geno <- geno %>% pivot_wider(names_from = c(marker,chr,!!sym(pos)),values_from = Geno,names_sep=",")
+ geno <- geno %>% mutate(id=as.character(id))
+ geno <- geno %>% rename("id,,"=id)
#merge with phenotype file
pheno <- pheno %>% mutate_all(as.character)
colnames(pheno) <- str_c(colnames(pheno),",,")
- qtl_file <- right_join(pheno,geno,by=c("Ind,,"="Sample.ID,,"))
+ qtl_file <- right_join(pheno,geno,by=c("Ind,,"="id,,"))
#prepare file
qtl_file <- rbind(colnames(qtl_file),qtl_file)
diff --git a/stuart_0.1.0.tar.gz b/stuart_0.1.0.tar.gz
index c0f464039673569fe02a33fa8028029a57a5ce7b..0574719a0ca2ebd5501a2b4295da59a4b5a87746 100644
Binary files a/stuart_0.1.0.tar.gz and b/stuart_0.1.0.tar.gz differ
diff --git a/vignettes/stuaRt.Rmd b/vignettes/stuaRt.Rmd
index 2dfb70edac53e76fd1e666150ea7dd15d9442f65..e73872a8f734ba8177b36fc84e013586614d4848 100755
--- a/vignettes/stuaRt.Rmd
+++ b/vignettes/stuaRt.Rmd
@@ -133,7 +133,7 @@ strains %>% filter(marker %in% c("gJAX00038569","gJAX00425031","gUNC12245354","g
After excluding the problematic markers, we can create the R/qtl file. The individuals must have the same ID in the geno and in the pheno file. If there is a prefix in the geno file that must be removed in order to acheive this, you can use the "prefix" argument. The "path" argument can be used in order to create a CSV file that you can laod with `qtl::read.cross`.
-```{r write_qtl,eval=F}
+```{r 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]