From 9e9e9002da3e4a409001d79992f03dd940702532 Mon Sep 17 00:00:00 2001
From: Marie Bourdon <mariefbourdon@gmail.com>
Date: Tue, 11 Jan 2022 12:46:46 +0100
Subject: [PATCH] modifs na prop + vignette
---
.Rproj.user/9DAE6990/pcs/source-pane.pper | 2 +-
.../9DAE6990/pcs/windowlayoutstate.pper | 12 ++++----
.Rproj.user/9DAE6990/pcs/workbench-pane.pper | 4 +--
.Rproj.user/9DAE6990/persistent-state | 2 +-
.Rproj.user/9DAE6990/rmd-outputs | 4 +--
.Rproj.user/9DAE6990/sources/prop/INDEX | 1 +
.Rproj.user/shared/notebooks/paths | 1 +
R/mark_prop.R | 20 ++++++--------
stuart_1.0.5.tar.gz | Bin 1431959100 -> 1994689302 bytes
vignettes/screenshot_newmap.png | Bin 0 -> 30377 bytes
vignettes/stuart.Rmd | 26 +++++++++++++++---
11 files changed, 45 insertions(+), 27 deletions(-)
create mode 100644 vignettes/screenshot_newmap.png
diff --git a/.Rproj.user/9DAE6990/pcs/source-pane.pper b/.Rproj.user/9DAE6990/pcs/source-pane.pper
index d3d70fa..3249574 100644
--- a/.Rproj.user/9DAE6990/pcs/source-pane.pper
+++ b/.Rproj.user/9DAE6990/pcs/source-pane.pper
@@ -1,3 +1,3 @@
{
- "activeTab" : 6
+ "activeTab" : 2
}
\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/pcs/windowlayoutstate.pper b/.Rproj.user/9DAE6990/pcs/windowlayoutstate.pper
index 19ed75d..7f81dbc 100644
--- a/.Rproj.user/9DAE6990/pcs/windowlayoutstate.pper
+++ b/.Rproj.user/9DAE6990/pcs/windowlayoutstate.pper
@@ -1,14 +1,14 @@
{
"left" : {
- "panelheight" : 762,
- "splitterpos" : 199,
+ "panelheight" : 1402,
+ "splitterpos" : 366,
"topwindowstate" : "NORMAL",
- "windowheight" : 800
+ "windowheight" : 1440
},
"right" : {
- "panelheight" : 762,
- "splitterpos" : 479,
+ "panelheight" : 1402,
+ "splitterpos" : 882,
"topwindowstate" : "NORMAL",
- "windowheight" : 800
+ "windowheight" : 1440
}
}
\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/pcs/workbench-pane.pper b/.Rproj.user/9DAE6990/pcs/workbench-pane.pper
index b15bf23..b9fcffa 100644
--- a/.Rproj.user/9DAE6990/pcs/workbench-pane.pper
+++ b/.Rproj.user/9DAE6990/pcs/workbench-pane.pper
@@ -1,6 +1,6 @@
{
- "TabSet1" : 3,
- "TabSet2" : 0,
+ "TabSet1" : 1,
+ "TabSet2" : 3,
"TabZoom" : {
}
}
\ No newline at end of file
diff --git a/.Rproj.user/9DAE6990/persistent-state b/.Rproj.user/9DAE6990/persistent-state
index 598ea69..acadc07 100644
--- a/.Rproj.user/9DAE6990/persistent-state
+++ b/.Rproj.user/9DAE6990/persistent-state
@@ -1,6 +1,6 @@
build-last-errors="[]"
build-last-errors-base-dir="~/Documents/PhD/stuart_package/stuart/"
-build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source stuart\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* installing *source* package ‘stuart’ ...\\n\",\"type\":1},{\"output\":\"** using staged installation\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** data\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** moving datasets to lazyload DB\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** inst\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** byte-compile and prepare package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** installing vignettes\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from temporary location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from final location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\",\"type\":1},{\"output\":\"* DONE (stuart)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
+build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source stuart\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’\\n\",\"type\":1},{\"output\":\"* installing *source* package ‘stuart’ ...\\n\",\"type\":1},{\"output\":\"** using staged installation\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** data\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** moving datasets to lazyload DB\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** inst\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** byte-compile and prepare package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** installing vignettes\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from temporary location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded from final location\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\",\"type\":1},{\"output\":\"* DONE (stuart)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
compile_pdf_state="{\"errors\":[],\"output\":\"\",\"running\":false,\"tab_visible\":false,\"target_file\":\"\"}"
files.monitored-path=""
find-in-files-state="{\"handle\":\"\",\"input\":\"\",\"path\":\"\",\"regex\":true,\"results\":{\"file\":[],\"line\":[],\"lineValue\":[],\"matchOff\":[],\"matchOn\":[]},\"running\":false}"
diff --git a/.Rproj.user/9DAE6990/rmd-outputs b/.Rproj.user/9DAE6990/rmd-outputs
index 97de97a..3da60b5 100644
--- a/.Rproj.user/9DAE6990/rmd-outputs
+++ b/.Rproj.user/9DAE6990/rmd-outputs
@@ -1,5 +1,5 @@
-/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpZZZ4WE/preview-31873a42c16d.dir/stuaRt.html
-/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/Rtmp3VMULh/preview-1ced48fe920c.dir/stuaRt.html
+/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpbddlPL/preview-1b515493e142.dir/stuart.html
+
/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpNme5vw/preview-4c4321234d03.dir/stuaRt.html
/private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpZZZ4WE/preview-3187564b41ab.dir/stuaRt.html
diff --git a/.Rproj.user/9DAE6990/sources/prop/INDEX b/.Rproj.user/9DAE6990/sources/prop/INDEX
index c8854a6..736b651 100644
--- a/.Rproj.user/9DAE6990/sources/prop/INDEX
+++ b/.Rproj.user/9DAE6990/sources/prop/INDEX
@@ -1,4 +1,5 @@
%2FVolumes%2F%40Mouselab%2FZika%2FBackcross%2FGeno%2FBC_01.71_stuart.Rmd="73DD6D1F"
+%2FVolumes%2F%40Mouselab%2FZika%2FF2%2FF2_B6.CC001%2FQUGA%2FQUGA.Rmd="D7285907"
~%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"
diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
index 9a8495e..3457e0e 100644
--- a/.Rproj.user/shared/notebooks/paths
+++ b/.Rproj.user/shared/notebooks/paths
@@ -10,3 +10,4 @@
/Users/mariebourdon/Documents/PhD/stuart_package/stuart/man/mark_prop.Rd="893B273D"
/Users/mariebourdon/Documents/PhD/stuart_package/stuart/vignettes/stuaRt.Rmd="DA6206CB"
/Users/mariebourdon/Documents/PhD/stuart_package/stuart/vignettes/stuart.Rmd="54D793B9"
+/Volumes/@Mouselab/Zika/F2/F2_B6.CC001/QUGA/QUGA.Rmd="7EACFFBF"
diff --git a/R/mark_prop.R b/R/mark_prop.R
index a10ec6b..0d756df 100755
--- a/R/mark_prop.R
+++ b/R/mark_prop.R
@@ -26,7 +26,7 @@
#### mark_prop ####
## excludes markers depending on proportions of homo/hetorozygous
-mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NULL,heteroX=NULL,na=0.5){
+mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NULL,heteroX=NULL){
#calculate total number of individuals genotyped for each marker
tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
@@ -59,8 +59,7 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NUL
tab <- tab %>% mutate(p_NA = n_NA/(n_geno+n_NA))
tab <- tab %>%
- mutate(exclude_prop=case_when(p_NA > na ~ 1,
- T ~ 0))
+ mutate(exclude_prop=0)
#stock colnames to join
names <- colnames(tab)
@@ -73,8 +72,7 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NUL
tab <- tab %>% mutate(p_HT = n_HT/n_geno)
tab <- tab %>%
- mutate(exclude_prop=case_when(p_NA > na ~ 1,
- !chr %in% c("X","Y","M") & cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
+ mutate(exclude_prop=case_when(!chr %in% c("X","Y","M") & cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
!chr %in% c("X","Y","M") & cross=="N2" & ((p_HM2 == 0 & p_HM1 < homo) |
(p_HM1 == 0 & p_HM2 < homo) |
(p_HT < hetero) |
@@ -88,8 +86,8 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NUL
mutate(exclude_prop=case_when(chr == "X" & p_HM1 >= p_HM2 & !between(p_HM1,homo1X[1],homo1X[2]) ~ 1,
chr == "X" & p_HM2 > p_HM1 & !between(p_HM2,homo1X[1],homo1X[2]) ~ 1,
T ~ exclude_prop
- )
- )
+ )
+ )
}
if(is.null(homo2X)==FALSE){
@@ -97,16 +95,16 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,homo1X=NULL,homo2X=NUL
mutate(exclude_prop=case_when(chr == "X" & p_HM1 >= p_HM2 & !between(p_HM2,homo2X[1],homo2X[2]) ~ 1,
chr == "X" & p_HM2 > p_HM1 & !between(p_HM1,homo2X[1],homo2X[2]) ~ 1,
T ~ exclude_prop
- )
- )
+ )
+ )
}
if(is.null(heteroX)==FALSE){
tab <- tab %>%
mutate(exclude_prop=case_when(chr == "X" & p_HM1 >= p_HM2 & !between(p_HT,heteroX[1],heteroX[2]) ~ 1,
T ~ exclude_prop
- )
- )
+ )
+ )
}
#exclude with pval chisq.test
diff --git a/stuart_1.0.5.tar.gz b/stuart_1.0.5.tar.gz
index ffe005a89d01aa88b963831fc718ece038c1e233..c74c1bff8ed4a413106168806a91ca21aae2f4be 100644
GIT binary patch