From 716a13935c8a4b998862f4e4e6e33a1ecde409cb Mon Sep 17 00:00:00 2001
From: Marie Bourdon <mariefbourdon@gmail.com>
Date: Mon, 7 Jun 2021 12:28:58 +0200
Subject: [PATCH] add modif to do
---
.Rproj.user/9DAE6990/pcs/source-pane.pper | 2 +-
.Rproj.user/9DAE6990/rmd-outputs | 3 +-
.../sources/{s-39B546A6 => per/t}/1656F55 | 4 +-
.../{s-39B546A6 => per/t}/1656F55-contents | 0
.../sources/{s-39B546A6 => per/t}/42D37312 | 10 +-
.../{s-39B546A6 => per/t}/42D37312-contents | 1 +
.../sources/{s-39B546A6 => per/t}/45D91D58 | 4 +-
.../{s-39B546A6 => per/t}/45D91D58-contents | 0
.../sources/{s-39B546A6 => per/t}/65C9B72B | 4 +-
.../{s-39B546A6 => per/t}/65C9B72B-contents | 0
.../sources/{s-39B546A6 => per/t}/76AC3EC | 8 +-
.../{s-39B546A6 => per/t}/76AC3EC-contents | 0
.../sources/{s-39B546A6 => per/t}/96AB3736 | 10 +-
.../{s-39B546A6 => per/t}/96AB3736-contents | 0
.../sources/{s-39B546A6 => per/t}/A6A5703A | 2 +-
.../{s-39B546A6 => per/t}/A6A5703A-contents | 0
.../sources/{s-39B546A6 => per/t}/B86C81D8 | 4 +-
.../{s-39B546A6 => per/t}/B86C81D8-contents | 0
.../sources/{s-39B546A6 => per/t}/C5228C18 | 4 +-
.../{s-39B546A6 => per/t}/C5228C18-contents | 0
.../sources/{s-39B546A6 => per/t}/C81C94E6 | 2 +-
.../{s-39B546A6 => per/t}/C81C94E6-contents | 0
.Rproj.user/9DAE6990/sources/prop/430FE7D7 | 4 +
.Rproj.user/9DAE6990/sources/prop/524B281F | 4 +
.Rproj.user/9DAE6990/sources/prop/52B275C1 | 4 +
.Rproj.user/9DAE6990/sources/prop/58D83345 | 4 +
.Rproj.user/9DAE6990/sources/prop/A58355B1 | 4 +
.Rproj.user/9DAE6990/sources/prop/B873B132 | 4 +
.Rproj.user/9DAE6990/sources/prop/B92E179B | 5 +
.Rproj.user/9DAE6990/sources/prop/C4894908 | 5 +
.Rproj.user/9DAE6990/sources/prop/DB7C2433 | 4 +
.Rproj.user/9DAE6990/sources/prop/E7505D7B | 4 +
.Rproj.user/9DAE6990/sources/prop/INDEX | 10 ++
.../sources/s-39B546A6/17AE345-contents | 0
.../sources/s-39B546A6/47AFB64-contents | 0
.../sources/s-39B546A6/4A9D04E-contents | 0
.../sources/s-39B546A6/6B5DE0D4-contents | 0
.../sources/s-39B546A6/7E4482C6-contents | 8 -
.../sources/s-39B546A6/806AAC34-contents | 0
.../sources/s-39B546A6/81311FDE-contents | 137 ------------------
.../sources/s-39B546A6/8DB3123E-contents | 0
.../sources/s-39B546A6/907DF1D3-contents | 55 -------
.../sources/s-39B546A6/9E3EC0FD-contents | 13 --
.../sources/s-39B546A6/C2CE7FEA-contents | 0
.../sources/s-39B546A6/C6286151-contents | 56 -------
.../sources/s-39B546A6/D49EE59C-contents | 0
.../sources/s-39B546A6/E7584E4F-contents | 0
.../9DAE6990/sources/s-39B546A6/lock_file | 0
.Rproj.user/shared/notebooks/paths | 7 +-
R/mark_prop.R | 1 +
50 files changed, 84 insertions(+), 303 deletions(-)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/1656F55 (85%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/1656F55-contents (100%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/42D37312 (67%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/42D37312-contents (98%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/45D91D58 (86%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/45D91D58-contents (100%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/65C9B72B (86%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/65C9B72B-contents (100%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/76AC3EC (73%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/76AC3EC-contents (100%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/96AB3736 (68%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/96AB3736-contents (100%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/A6A5703A (89%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/A6A5703A-contents (100%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/B86C81D8 (85%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/B86C81D8-contents (100%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/C5228C18 (86%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/C5228C18-contents (100%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/C81C94E6 (90%)
rename .Rproj.user/9DAE6990/sources/{s-39B546A6 => per/t}/C81C94E6-contents (100%)
create mode 100644 .Rproj.user/9DAE6990/sources/prop/430FE7D7
create mode 100644 .Rproj.user/9DAE6990/sources/prop/524B281F
create mode 100644 .Rproj.user/9DAE6990/sources/prop/52B275C1
create mode 100644 .Rproj.user/9DAE6990/sources/prop/58D83345
create mode 100644 .Rproj.user/9DAE6990/sources/prop/A58355B1
create mode 100644 .Rproj.user/9DAE6990/sources/prop/B873B132
create mode 100644 .Rproj.user/9DAE6990/sources/prop/B92E179B
create mode 100644 .Rproj.user/9DAE6990/sources/prop/C4894908
create mode 100644 .Rproj.user/9DAE6990/sources/prop/DB7C2433
create mode 100644 .Rproj.user/9DAE6990/sources/prop/E7505D7B
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/17AE345-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/47AFB64-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/4A9D04E-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/6B5DE0D4-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/7E4482C6-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/806AAC34-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/81311FDE-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/8DB3123E-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/907DF1D3-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/9E3EC0FD-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/C2CE7FEA-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/C6286151-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/D49EE59C-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/E7584E4F-contents
delete mode 100644 .Rproj.user/9DAE6990/sources/s-39B546A6/lock_file
diff --git a/.Rproj.user/9DAE6990/pcs/source-pane.pper b/.Rproj.user/9DAE6990/pcs/source-pane.pper
index 1743e40..d3d70fa 100644
--- a/.Rproj.user/9DAE6990/pcs/source-pane.pper
+++ b/.Rproj.user/9DAE6990/pcs/source-pane.pper
@@ -1,3 +1,3 @@
{
- "activeTab" : 0
+ "activeTab" : 6
}
\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/rmd-outputs b/.Rproj.user/9DAE6990/rmd-outputs
index dd18ecc..47f8c13 100644
--- a/.Rproj.user/9DAE6990/rmd-outputs
+++ b/.Rproj.user/9DAE6990/rmd-outputs
@@ -1,7 +1,8 @@
/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/Rtmp3VMULh/preview-1ced414f7aab.dir/stuaRt.html
/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/Rtmp3VMULh/preview-1ced48fe920c.dir/stuaRt.html
-
/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpNme5vw/preview-4c4321234d03.dir/stuaRt.html
+
+
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/1656F55 b/.Rproj.user/9DAE6990/sources/per/t/1656F55
similarity index 85%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/1656F55
rename to .Rproj.user/9DAE6990/sources/per/t/1656F55
index 7aaecc2..8e20769 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/1656F55
+++ b/.Rproj.user/9DAE6990/sources/per/t/1656F55
@@ -9,11 +9,11 @@
"id" : "1656F55",
"lastKnownWriteTime" : 1622640147,
"last_content_update" : 1622640147,
- "path" : "~/stuart_package/stuart/R/geno_strains.R",
+ "path" : "~/Documents/PhD/stuart_R/stuart/R/geno_strains.R",
"project_path" : "R/geno_strains.R",
"properties" : {
"cursorPosition" : "22,39",
- "scrollLine" : "7"
+ "scrollLine" : "0"
},
"read_only" : false,
"read_only_alternatives" : [
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/1656F55-contents b/.Rproj.user/9DAE6990/sources/per/t/1656F55-contents
similarity index 100%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/1656F55-contents
rename to .Rproj.user/9DAE6990/sources/per/t/1656F55-contents
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/42D37312 b/.Rproj.user/9DAE6990/sources/per/t/42D37312
similarity index 67%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/42D37312
rename to .Rproj.user/9DAE6990/sources/per/t/42D37312
index 583c1f7..bb16ed6 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/42D37312
+++ b/.Rproj.user/9DAE6990/sources/per/t/42D37312
@@ -5,14 +5,14 @@
"dirty" : false,
"encoding" : "UTF-8",
"folds" : "",
- "hash" : "0",
+ "hash" : "3094972460",
"id" : "42D37312",
- "lastKnownWriteTime" : 1622465534,
- "last_content_update" : 1622465534,
- "path" : "~/stuart_package/stuart/R/mark_prop.R",
+ "lastKnownWriteTime" : 1623061718,
+ "last_content_update" : 1623061718577,
+ "path" : "~/Documents/PhD/stuart_R/stuart/R/mark_prop.R",
"project_path" : "R/mark_prop.R",
"properties" : {
- "cursorPosition" : "2,104",
+ "cursorPosition" : "16,28",
"scrollLine" : "0"
},
"read_only" : false,
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/42D37312-contents b/.Rproj.user/9DAE6990/sources/per/t/42D37312-contents
similarity index 98%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/42D37312-contents
rename to .Rproj.user/9DAE6990/sources/per/t/42D37312-contents
index a0827e8..8af6e84 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/42D37312-contents
+++ 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))
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58 b/.Rproj.user/9DAE6990/sources/per/t/45D91D58
similarity index 86%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58
rename to .Rproj.user/9DAE6990/sources/per/t/45D91D58
index f68fb4c..e376a74 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58
+++ b/.Rproj.user/9DAE6990/sources/per/t/45D91D58
@@ -9,11 +9,11 @@
"id" : "45D91D58",
"lastKnownWriteTime" : 1622648301,
"last_content_update" : 1622648301329,
- "path" : "~/stuart_package/stuart/R/write_rqtl.R",
+ "path" : "~/Documents/PhD/stuart_R/stuart/R/write_rqtl.R",
"project_path" : "R/write_rqtl.R",
"properties" : {
"cursorPosition" : "84,18",
- "scrollLine" : "94"
+ "scrollLine" : "0"
},
"read_only" : false,
"read_only_alternatives" : [
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58-contents b/.Rproj.user/9DAE6990/sources/per/t/45D91D58-contents
similarity index 100%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58-contents
rename to .Rproj.user/9DAE6990/sources/per/t/45D91D58-contents
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/65C9B72B b/.Rproj.user/9DAE6990/sources/per/t/65C9B72B
similarity index 86%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/65C9B72B
rename to .Rproj.user/9DAE6990/sources/per/t/65C9B72B
index 51dacef..c988561 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/65C9B72B
+++ b/.Rproj.user/9DAE6990/sources/per/t/65C9B72B
@@ -9,11 +9,11 @@
"id" : "65C9B72B",
"lastKnownWriteTime" : 1622642120,
"last_content_update" : 1622642120783,
- "path" : "~/stuart_package/stuart/R/tab_mark.R",
+ "path" : "~/Documents/PhD/stuart_R/stuart/R/tab_mark.R",
"project_path" : "R/tab_mark.R",
"properties" : {
"cursorPosition" : "43,27",
- "scrollLine" : "29",
+ "scrollLine" : "0",
"source_window_id" : ""
},
"read_only" : false,
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/65C9B72B-contents b/.Rproj.user/9DAE6990/sources/per/t/65C9B72B-contents
similarity index 100%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/65C9B72B-contents
rename to .Rproj.user/9DAE6990/sources/per/t/65C9B72B-contents
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/76AC3EC b/.Rproj.user/9DAE6990/sources/per/t/76AC3EC
similarity index 73%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/76AC3EC
rename to .Rproj.user/9DAE6990/sources/per/t/76AC3EC
index 19b279e..34ddaca 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/76AC3EC
+++ b/.Rproj.user/9DAE6990/sources/per/t/76AC3EC
@@ -5,11 +5,11 @@
"dirty" : false,
"encoding" : "UTF-8",
"folds" : "",
- "hash" : "0",
+ "hash" : "143869640",
"id" : "76AC3EC",
- "lastKnownWriteTime" : 1622644628,
- "last_content_update" : 1622644628349,
- "path" : "~/stuart_package/stuart/R/mark_match.R",
+ "lastKnownWriteTime" : 1623060553,
+ "last_content_update" : 1623060553,
+ "path" : "~/Documents/PhD/stuart_R/stuart/R/mark_match.R",
"project_path" : "R/mark_match.R",
"properties" : {
"cursorPosition" : "20,46",
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/76AC3EC-contents b/.Rproj.user/9DAE6990/sources/per/t/76AC3EC-contents
similarity index 100%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/76AC3EC-contents
rename to .Rproj.user/9DAE6990/sources/per/t/76AC3EC-contents
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736 b/.Rproj.user/9DAE6990/sources/per/t/96AB3736
similarity index 68%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736
rename to .Rproj.user/9DAE6990/sources/per/t/96AB3736
index ff216ba..84a57ef 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736
+++ b/.Rproj.user/9DAE6990/sources/per/t/96AB3736
@@ -7,14 +7,14 @@
"folds" : "",
"hash" : "2014255563",
"id" : "96AB3736",
- "lastKnownWriteTime" : 1622648726,
- "last_content_update" : 1622648726992,
- "path" : "~/stuart_package/stuart/vignettes/stuaRt.Rmd",
+ "lastKnownWriteTime" : 1623060592,
+ "last_content_update" : 1623060592,
+ "path" : "~/Documents/PhD/stuart_R/stuart/vignettes/stuaRt.Rmd",
"project_path" : "vignettes/stuaRt.Rmd",
"properties" : {
"cursorPosition" : "135,15",
- "last_setup_crc32" : "39B546A65bfca283",
- "scrollLine" : "130"
+ "last_setup_crc32" : "",
+ "scrollLine" : "111"
},
"read_only" : false,
"read_only_alternatives" : [
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736-contents b/.Rproj.user/9DAE6990/sources/per/t/96AB3736-contents
similarity index 100%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736-contents
rename to .Rproj.user/9DAE6990/sources/per/t/96AB3736-contents
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/A6A5703A b/.Rproj.user/9DAE6990/sources/per/t/A6A5703A
similarity index 89%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/A6A5703A
rename to .Rproj.user/9DAE6990/sources/per/t/A6A5703A
index f1dd731..e498a6c 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/A6A5703A
+++ b/.Rproj.user/9DAE6990/sources/per/t/A6A5703A
@@ -9,7 +9,7 @@
"id" : "A6A5703A",
"lastKnownWriteTime" : 1622641746,
"last_content_update" : 1622641746302,
- "path" : "~/stuart_package/stuart/R/stuart_tab-data.R",
+ "path" : "~/Documents/PhD/stuart_R/stuart/R/stuart_tab-data.R",
"project_path" : "R/stuart_tab-data.R",
"properties" : {
"cursorPosition" : "8,12",
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/A6A5703A-contents b/.Rproj.user/9DAE6990/sources/per/t/A6A5703A-contents
similarity index 100%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/A6A5703A-contents
rename to .Rproj.user/9DAE6990/sources/per/t/A6A5703A-contents
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/B86C81D8 b/.Rproj.user/9DAE6990/sources/per/t/B86C81D8
similarity index 85%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/B86C81D8
rename to .Rproj.user/9DAE6990/sources/per/t/B86C81D8
index 66bd8e5..b6a9d87 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/B86C81D8
+++ b/.Rproj.user/9DAE6990/sources/per/t/B86C81D8
@@ -5,11 +5,11 @@
"dirty" : false,
"encoding" : "UTF-8",
"folds" : "",
- "hash" : "0",
+ "hash" : "4129306061",
"id" : "B86C81D8",
"lastKnownWriteTime" : 1622646597,
"last_content_update" : 1622646597951,
- "path" : "~/stuart_package/stuart/R/mark_allele.R",
+ "path" : "~/Documents/PhD/stuart_R/stuart/R/mark_allele.R",
"project_path" : "R/mark_allele.R",
"properties" : {
"cursorPosition" : "23,55",
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/B86C81D8-contents b/.Rproj.user/9DAE6990/sources/per/t/B86C81D8-contents
similarity index 100%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/B86C81D8-contents
rename to .Rproj.user/9DAE6990/sources/per/t/B86C81D8-contents
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/C5228C18 b/.Rproj.user/9DAE6990/sources/per/t/C5228C18
similarity index 86%
rename from .Rproj.user/9DAE6990/sources/s-39B546A6/C5228C18
rename to .Rproj.user/9DAE6990/sources/per/t/C5228C18
index 57f6d66..b8720f3 100644
--- a/.Rproj.user/9DAE6990/sources/s-39B546A6/C5228C18
+++ b/.Rproj.user/9DAE6990/sources/per/t/C5228C18
@@ -5,11 +5,11 @@
"dirty" : false,
"encoding" : "UTF-8",
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diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/17AE345-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/17AE345-contents
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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 e69de29..0000000
diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/4A9D04E-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/4A9D04E-contents
deleted file mode 100644
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diff --git a/.Rproj.user/9DAE6990/sources/s-39B546A6/6B5DE0D4-contents b/.Rproj.user/9DAE6990/sources/s-39B546A6/6B5DE0D4-contents
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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 fd50eb0..0000000
--- 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 e69de29..0000000
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 612c27d..0000000
--- 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 e69de29..0000000
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 d4104d0..0000000
--- 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 902e043..0000000
--- 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 e69de29..0000000
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 0035346..0000000
--- 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
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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 e69de29..0000000
diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
index 7779f20..f483eb7 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 a0827e8..8af6e84 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))
--
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