mark_prop chi2 N2

.Rhistory

-place <- c()
-previous <- c()
-follow <- c()
-#get information in newmap
-for(i in names(map)){
-marker <- c(marker,names(map[[i]]))
-chr <- c(chr,rep(i,times=length(map[[i]])))
-pos <- c(pos,unname(map[[i]]))
-place <- c(place,"first",rep("middle",times=(length(map[[i]])-2)),"last")
-prev <- c(NA,unname(map[[i]])[1:length(map[[i]])-1])
-previous <- c(previous,prev)
-fol <- c(unname(map[[i]])[2:length(map[[i]])],NA)
-follow <- c(follow,fol)
-}
-tab_map <- tibble(marker = marker,
-chr = chr,
-place = place,
-pos = pos,
-previous = pos-previous,
-follow = follow-pos)
-tab_map <- tab_map %>% mutate(exclude=case_when(place == "first" & follow > 100 ~ 1,
-place == "middle" & previous > 100 & follow > 100 ~ 1,
-place == "last" & previous > 100 ~ 1,
-T ~ 0))
 bad_markers <- tab_map %>% filter(exclude == 1) %>% pull(marker)
 }
 mark_estmap <- function(map,dist=100){
@@ -510,3 +486,27 @@ rm(stuart_cross)
 library(qtl)
 data(stuart_cross)
 summary(stuart_cross)
+setwd("~/Documents/stuart_package/stuart")
+devtools::build(path=".",vignettes=FALSE)
+devtools::build_vignettes()
+devtools::build_manual()
+library(stuart)
+mark_prop
+devtools::build_manual(path=".")
+library(dplyr)
+library(stuart)
+annot_mini <- read.csv(url("https://raw.githubusercontent.com/kbroman/MUGAarrays/master/UWisc/mini_uwisc_v2.csv"))
+data(genos)
+summary(genos)
+data(phenos)
+summary(phenos)
+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) %>% print.data.frame()
+genos <- genos %>% filter(!Sample.ID %in% c("StrainsA_1", "StrainsA_2",
+"StrainsB_1","StrainsB_2"))
+# how to use the function:
+# stuart_tab <- tab_mark(genos)
+data(stuart_tab)
+summary(stuart_tab)
+View(stuart_tab)

R/mark_prop.R

@@ -61,27 +61,36 @@ mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
                                     T ~ exclude_prop
       ))
 
-  #exclude with pval chisq.test
+    #exclude with pval chisq.test
   } else if(is.na(pval)==FALSE){
 
     #if cross F2
     if(cross=="F2"){
+      #chisq test
       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=all_of(names))
 
+      #convert in score
       tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
                                                    T ~ exclude_prop))
 
       #if cross N2
     } else if(cross=="N2"){
+
+      #stock homozygous data in a new column (either n_HM1 or n-<hm2)
+      tab <- tab %>% mutate(n_hm = case_when(n_HM1>n_HM2 ~ n_HM1,
+                                             T ~ n_HM2))
+
+      #chisq test
       tab <- tab %>% filter(p_NA != 1) %>% rowwise() %>%
-        mutate(.,chi_pval = tibble(n_HM1,n_HT) %>%
-                 chisq.test(p=c(0.5,0.5)) %>% .$p.value) %>%
-        full_join(.,tab,by=all_of(names))
+        mutate(.,chi_pval =chisq.test(x=c(n_hm,n_HT),p=c(0.5,0.5)) %>% .$p.value) %>%
+        full_join(.,tab,by=c(all_of(names),"n_hm"))
 
+      #convert in score
       tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+                                                   (n_HM1 !=0 & n_HM2 != 0) ~ 1,
                                                    T ~ exclude_prop))
     }