add manual

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

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+~%2Fstuart_package%2Fstuart%2FNAMESPACE="AE613167"
+~%2Fstuart_package%2Fstuart%2FR%2Fmark_poly.R="3A328548"
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.Rproj.user/9DAE6990/sources/s-31136BFE/32FAC663-contents

-## ---- 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)
-

.Rproj.user/9DAE6990/sources/s-31136BFE/45D91D58 → .Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58

@@ -5,20 +5,20 @@
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     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "0",
+    "hash" : "3120719904",
     "id" : "45D91D58",
-    "lastKnownWriteTime" : 1622539449,
-    "last_content_update" : 1622539449402,
+    "lastKnownWriteTime" : 1622621980,
+    "last_content_update" : 1622621980790,
     "path" : "~/stuart_package/stuart/R/write_rqtl.R",
     "project_path" : "R/write_rqtl.R",
     "properties" : {
-        "cursorPosition" : "100,50",
-        "scrollLine" : "96"
+        "cursorPosition" : "48,32",
+        "scrollLine" : "33"
     },
     "read_only" : false,
     "read_only_alternatives" : [
     ],
-    "relative_order" : 1,
+    "relative_order" : 5,
     "source_on_save" : false,
     "source_window" : "",
     "type" : "r_source"

.Rproj.user/9DAE6990/sources/s-31136BFE/45D91D58-contents → .Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58-contents

@@ -48,7 +48,7 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
 
   #keep parental lines genotypes
   colnames(ref) <- make.names(colnames(ref))
-  ref <- ref %>% select(marker,chr,bp_mm10,!!sym(pos),!!sym(par1),!!sym(par2))
+  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"))
@@ -92,12 +92,12 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
 
 
   #keep positions of markers
-  markers <- geno %>% select(SNP.Name,chr,bp_mm10,!!sym(pos)) %>% distinct()
-  markers <- markers %>% arrange(chr,bp_mm10)
+  markers <- geno %>% select(SNP.Name,chr,!!sym(pos)) %>% distinct()
+  markers <- markers %>% arrange(chr,!!sym(pos))
 
 
   #keep only interesting columns in geno file
-  geno <- geno %>% arrange(chr,bp_mm10)
+  geno <- geno %>% arrange(chr,!!sym(pos))
   geno <- geno %>% select(SNP.Name,Sample.ID,Geno)
 
   #remove prefix

.Rproj.user/9DAE6990/sources/s-31136BFE/47AFB64 → .Rproj.user/9DAE6990/sources/s-39B546A6/47AFB64

@@ -26,7 +26,7 @@
     "read_only" : false,
     "read_only_alternatives" : [
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-    "relative_order" : 5,
+    "relative_order" : 6,
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     "type" : "r_dataframe"

.Rproj.user/9DAE6990/sources/s-31136BFE/4A9D04E → .Rproj.user/9DAE6990/sources/s-39B546A6/4A9D04E

@@ -12,21 +12,21 @@
     "path" : null,
     "project_path" : null,
     "properties" : {
-        "cacheKey" : "2EEA0644",
+        "cacheKey" : "F7A5FD33",
         "caption" : "strains",
-        "contentUrl" : "grid_resource/gridviewer.html?env=&obj=strains&cache_key=2EEA0644",
-        "displayedObservations" : 11125,
+        "contentUrl" : "grid_resource/gridviewer.html?env=&obj=strains&cache_key=F7A5FD33",
+        "displayedObservations" : "11125",
         "environment" : "",
         "expression" : "strains",
         "object" : "strains",
-        "preview" : 0,
-        "totalObservations" : 11125,
-        "variables" : 14
+        "preview" : "0",
+        "totalObservations" : "11125",
+        "variables" : "14"
     },
     "read_only" : false,
     "read_only_alternatives" : [
     ],
-    "relative_order" : 6,
+    "relative_order" : 3,
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     "source_window" : "",
     "type" : "r_dataframe"

.Rproj.user/9DAE6990/sources/s-31136BFE/806AAC34 → .Rproj.user/9DAE6990/sources/s-39B546A6/806AAC34

@@ -26,7 +26,7 @@
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.Rproj.user/9DAE6990/sources/s-31136BFE/96AB3736 → .Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736

@@ -7,19 +7,19 @@
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+    "lastKnownWriteTime" : 1622624631,
+    "last_content_update" : 1622624631694,
     "path" : "~/stuart_package/stuart/vignettes/stuaRt.Rmd",
     "project_path" : "vignettes/stuaRt.Rmd",
     "properties" : {
-        "cursorPosition" : "128,16",
-        "last_setup_crc32" : "31136BFE5bfca283",
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+        "scrollLine" : "44"
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-    "relative_order" : 2,
+    "relative_order" : 1,
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     "source_window" : "",
     "type" : "r_markdown"

.Rproj.user/9DAE6990/sources/s-39B546A6/9E3EC0FD

+{
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+    "contents" : "",
+    "created" : 1622622953119.000,
+    "dirty" : false,
+    "encoding" : "UTF-8",
+    "folds" : "",
+    "hash" : "2767839831",
+    "id" : "9E3EC0FD",
+    "lastKnownWriteTime" : 1622539469,
+    "last_content_update" : 1622539469,
+    "path" : "~/stuart_package/stuart/NAMESPACE",
+    "project_path" : "NAMESPACE",
+    "properties" : {
+    },
+    "read_only" : true,
+    "read_only_alternatives" : [
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+    "relative_order" : 8,
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+    "source_window" : "",
+    "type" : "r_namespace"
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