add tidyselect in imports

.Rhistory

-print(tab)
-}
-tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
+devtools::build_manual(path=".")
+remove.packages("stuart")
+devtools::install_gitlab(repo="mouselab/stuart",host="gitlab.pasteur.fr")
+library(stuart)
+View(annot_mini)
+annot_mini %>% filter(is.na(chr)==FALSE) %>% filter(is.na(cM_cox)==TRUE)
+devtools::build(path=".",vignettes=FALSE)
+library(stuart)
+write_rqtl
+chisq.test(c(20,23),p=c(0.5,0.5))
 mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
-#calculate total number of individuals genotyped for each marker
-tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
 #stock colnames to join
 names <- colnames(tab)
-print(names)
+#calculate total number of individuals genotyped for each marker
+tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
 #stop if cross != "F2" or "N2"
 if(!cross %in% c("F2","N2")){
 stop("Cross must be F2 or N2")
@@ -37,22 +43,37 @@ T ~ exclude_prop
 #exclude with pval chisq.test
 ## NEED TO ADD THIS FILTER IF CROSS = N2
 if(is.na(pval)==FALSE){
+#if cross F2
+if(cross=="F2"){
 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)) %>% .$p.value) %>%
 full_join(.,tab,by=all_of(names))
 tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
 T ~ exclude_prop))
+} else if(cross=="N2"){
+ab <- tab %>% filter(p_NA != 1) %>% rowwise() %>%
+mutate(.,chi_pval = tibble(n_HM1,n_HT) %>%
+chisq.test(p=c(0.5,0.5)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
+}
 }
-print(tab)
 tab <- tab %>% select(all_of(names),exclude_prop)
-print(tab)
+return(tab)
 }
-tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
+test <- tibble(marker=c("mark1","mark2","mark3","mark4"),)
+library(tidyverse)
+test <- tibble(marker=c("mark1","mark2","mark3","mark4"),allele_1=c(A,G,T,C),allele_2=c(T,T,A,G),n_HM1=c(48,45,1,26),n_HM2=c(0,0,0,0),n_HT=c(52,55,49,74))
+test <- tibble(marker=c("mark1","mark2","mark3","mark4"),allele_1=c("A","G","T","C"),allele_2=c("T","T","A","G"),n_HM1=c(48,45,1,26),n_HM2=c(0,0,0,0),n_HT=c(52,55,49,74))
+View(test)
+mark_prop(test,cross="N2",pval=0.05)
+test <- tibble(marker=c("mark1","mark2","mark3","mark4"),allele_1=c("A","G","T","C"),allele_2=c("T","T","A","G"),n_HM1=c(48,45,1,26),n_HM2=c(0,0,0,0),n_HT=c(52,55,49,74),n_NA=c(0,0,0,0))
+mark_prop(test,cross="N2",pval=0.05)
 mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
 #stock colnames to join
 names <- colnames(tab)
-print(names)
 #calculate total number of individuals genotyped for each marker
 tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
 #stop if cross != "F2" or "N2"
@@ -81,25 +102,205 @@ cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
 cross=="N2" & (p_HM1 < homo | p_HT < hetero) ~ 1,
 T ~ exclude_prop
 ))
+#exclude with pval chisq.test
+} else if(is.na(pval)==FALSE){
+#if cross F2
+if(cross=="F2"){
+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)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
+#if cross N2
+} else if(cross=="N2"){
+tab <- tab %>% filter(p_NA != 1) %>% rowwise() %>%
+mutate(.,chi_pval = tibble(n_HM1,n_HT) %>%
+chisq.test(p=c(0.5,0.5)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
+}
+}
+tab <- tab %>% select(all_of(names),exclude_prop)
+return(tab)
+}
+mark_prop(test,cross="N2",pval=0.05)
+mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
+#stock colnames to join
+names <- colnames(tab)
+#calculate total number of individuals genotyped for each marker
+tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
+#stop if cross != "F2" or "N2"
+if(!cross %in% c("F2","N2")){
+stop("Cross must be F2 or N2")
+}
+#stop of homo&hetero or pval not specified
+if((is.na(homo)==TRUE | is.na(hetero)==TRUE) & is.na(pval)==TRUE){
+stop("Arguments homo and hetero or argument pval must be specified")
 }
+#stop with prop of na
+#calculate proportion
+tab <- tab %>% mutate(p_NA = n_NA/(n_geno+n_NA))
+tab <- tab %>%
+mutate(exclude_prop=case_when(p_NA > na ~ 1,
+T ~ 0))
+print(tab)
+#exclude with prop of homo/hetero
+if(is.na(pval)==TRUE){
+#calculate proportion of each genotype
+tab <- tab %>% mutate(p_HM1 = n_HM1/n_geno)
+tab <- tab %>% mutate(p_HM2 = n_HM2/n_geno)
+tab <- tab %>% mutate(p_HT = n_HT/n_geno)
+tab <- tab %>%
+mutate(exclude_prop=case_when(p_NA > na ~ 1,
+cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
+cross=="N2" & (p_HM1 < homo | p_HT < hetero) ~ 1,
+T ~ exclude_prop
+))
 #exclude with pval chisq.test
-## NEED TO ADD THIS FILTER IF CROSS = N2
-if(is.na(pval)==FALSE){
+} else if(is.na(pval)==FALSE){
+#if cross F2
+if(cross=="F2"){
 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)) %>% .$p.value) %>%
 full_join(.,tab,by=all_of(names))
 tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
 T ~ exclude_prop))
+#if cross N2
+} else if(cross=="N2"){
+tab <- tab %>% filter(p_NA != 1) %>% rowwise() %>%
+mutate(.,chi_pval = tibble(n_HM1,n_HT) %>%
+chisq.test(p=c(0.5,0.5)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
+}
 }
+tab <- tab %>% select(all_of(names),exclude_prop)
+return(tab)
+}
+mark_prop(test,cross="N2",pval=0.05)
+mark_prop(test,cross="N2",homo=0.1,hetero=0.1)
+mark_prop(test,cross="F2",homo=0.1,hetero=0.1)
+mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
+#stock colnames to join
+names <- colnames(tab)
+#calculate total number of individuals genotyped for each marker
+tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
+#stop if cross != "F2" or "N2"
+if(!cross %in% c("F2","N2")){
+stop("Cross must be F2 or N2")
+}
+#stop of homo&hetero or pval not specified
+if((is.na(homo)==TRUE | is.na(hetero)==TRUE) & is.na(pval)==TRUE){
+stop("Arguments homo and hetero or argument pval must be specified")
+}
+#stop with prop of na
+#calculate proportion
+tab <- tab %>% mutate(p_NA = n_NA/(n_geno+n_NA))
+tab <- tab %>%
+mutate(exclude_prop=case_when(p_NA > na ~ 1,
+T ~ 0))
 print(tab)
+#exclude with prop of homo/hetero
+if(is.na(pval)==TRUE){
+#calculate proportion of each genotype
+tab <- tab %>% mutate(p_HM1 = n_HM1/n_geno)
+tab <- tab %>% mutate(p_HM2 = n_HM2/n_geno)
+tab <- tab %>% mutate(p_HT = n_HT/n_geno)
+tab <- tab %>%
+mutate(exclude_prop=case_when(p_NA > na ~ 1,
+cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
+cross=="N2" & (p_HM1 < homo | p_HT < hetero) ~ 1,
+T ~ exclude_prop
+))
+#exclude with pval chisq.test
+} else if(is.na(pval)==FALSE){
+#if cross F2
+if(cross=="F2"){
+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)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
+#if cross N2
+} else if(cross=="N2"){
+tab <- tab %>% filter(p_NA != 1) %>% rowwise() %>%
+mutate(.,chi_pval = tibble(n_HM1,n_HT) %>%
+chisq.test(p=c(0.5,0.5)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
+print(tab)
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
+}
+}
 tab <- tab %>% select(all_of(names),exclude_prop)
+return(tab)
+}
+mark_prop(test,cross="F2",pval=0.05)
+mark_prop(test,cross="N2",pval=0.05)
+View(test)
+mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
+#stock colnames to join
+names <- colnames(tab)
+#calculate total number of individuals genotyped for each marker
+tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
+#stop if cross != "F2" or "N2"
+if(!cross %in% c("F2","N2")){
+stop("Cross must be F2 or N2")
+}
+#stop of homo&hetero or pval not specified
+if((is.na(homo)==TRUE | is.na(hetero)==TRUE) & is.na(pval)==TRUE){
+stop("Arguments homo and hetero or argument pval must be specified")
+}
+#stop with prop of na
+#calculate proportion
+tab <- tab %>% mutate(p_NA = n_NA/(n_geno+n_NA))
+tab <- tab %>%
+mutate(exclude_prop=case_when(p_NA > na ~ 1,
+T ~ 0))
 print(tab)
+#exclude with prop of homo/hetero
+if(is.na(pval)==TRUE){
+#calculate proportion of each genotype
+tab <- tab %>% mutate(p_HM1 = n_HM1/n_geno)
+tab <- tab %>% mutate(p_HM2 = n_HM2/n_geno)
+tab <- tab %>% mutate(p_HT = n_HT/n_geno)
+tab <- tab %>%
+mutate(exclude_prop=case_when(p_NA > na ~ 1,
+cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
+cross=="N2" & (p_HM1 < homo | p_HT < hetero) ~ 1,
+T ~ exclude_prop
+))
+print(names)
+#exclude with pval chisq.test
+} else if(is.na(pval)==FALSE){
+#if cross F2
+if(cross=="F2"){
+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)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
+#if cross N2
+} else if(cross=="N2"){
+tab <- tab %>% filter(p_NA != 1) %>% rowwise() %>%
+mutate(.,chi_pval = tibble(n_HM1,n_HT) %>%
+chisq.test(p=c(0.5,0.5)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
+print(tab)
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
 }
-tab2 <- mark_match(stuart_tab,ref=strains)
-tab2 %>% filter(exclude_match==1)
-tab2 <- mark_poly(tab2)
-head(tab2)
+}
+tab <- tab %>% select(all_of(names),exclude_prop)
+return(tab)
+}
+mark_prop(test,cross="N2",pval=0.05)
 mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
 #stock colnames to join
 names <- colnames(tab)
@@ -120,6 +321,7 @@ tab <- tab %>% mutate(p_NA = n_NA/(n_geno+n_NA))
 tab <- tab %>%
 mutate(exclude_prop=case_when(p_NA > na ~ 1,
 T ~ 0))
+print(tab)
 #exclude with prop of homo/hetero
 if(is.na(pval)==TRUE){
 #calculate proportion of each genotype
@@ -132,320 +334,147 @@ cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
 cross=="N2" & (p_HM1 < homo | p_HT < hetero) ~ 1,
 T ~ exclude_prop
 ))
-}
 #exclude with pval chisq.test
-## NEED TO ADD THIS FILTER IF CROSS = N2
-if(is.na(pval)==FALSE){
+} else if(is.na(pval)==FALSE){
+#if cross F2
+if(cross=="F2"){
 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)) %>% .$p.value) %>%
 full_join(.,tab,by=all_of(names))
 tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
 T ~ exclude_prop))
-}
+#if cross N2
+} else if(cross=="N2"){
+tab <- tab %>% filter(p_NA != 1) %>% rowwise() %>%
+mutate(.,chi_pval = tibble(n_HM1,n_HT) %>%
+chisq.test(p=c(0.5,0.5)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
 print(tab)
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
+}
+}
 tab <- tab %>% select(all_of(names),exclude_prop)
+return(tab)
+}
+mark_prop(test,cross="N2",pval=0.05)
+mark_prop <- function(tab,cross,homo=NA,hetero=NA,pval=NA,na=0.5){
+#calculate total number of individuals genotyped for each marker
+tab <- tab %>% mutate(n_geno = (n_HM1 + n_HM2 + n_HT))
+#stop if cross != "F2" or "N2"
+if(!cross %in% c("F2","N2")){
+stop("Cross must be F2 or N2")
+}
+#stop of homo&hetero or pval not specified
+if((is.na(homo)==TRUE | is.na(hetero)==TRUE) & is.na(pval)==TRUE){
+stop("Arguments homo and hetero or argument pval must be specified")
+}
+#stop with prop of na
+#calculate proportion
+tab <- tab %>% mutate(p_NA = n_NA/(n_geno+n_NA))
+tab <- tab %>%
+mutate(exclude_prop=case_when(p_NA > na ~ 1,
+T ~ 0))
+print(tab)
+#stock colnames to join
+names <- colnames(tab)
+print(names)
+#exclude with prop of homo/hetero
+if(is.na(pval)==TRUE){
+#calculate proportion of each genotype
+tab <- tab %>% mutate(p_HM1 = n_HM1/n_geno)
+tab <- tab %>% mutate(p_HM2 = n_HM2/n_geno)
+tab <- tab %>% mutate(p_HT = n_HT/n_geno)
+tab <- tab %>%
+mutate(exclude_prop=case_when(p_NA > na ~ 1,
+cross=="F2" & (p_HM1 < homo | p_HM2 < homo | p_HT < hetero) ~ 1,
+cross=="N2" & (p_HM1 < homo | p_HT < hetero) ~ 1,
+T ~ exclude_prop
+))
+#exclude with pval chisq.test
+} else if(is.na(pval)==FALSE){
+#if cross F2
+if(cross=="F2"){
+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)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
+#if cross N2
+} else if(cross=="N2"){
+tab <- tab %>% filter(p_NA != 1) %>% rowwise() %>%
+mutate(.,chi_pval = tibble(n_HM1,n_HT) %>%
+chisq.test(p=c(0.5,0.5)) %>% .$p.value) %>%
+full_join(.,tab,by=all_of(names))
 print(tab)
+tab <- tab %>% mutate(exclude_prop=case_when(chi_pval < pval ~ 1,
+T ~ exclude_prop))
 }
-tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
-devtools::build(path=".",vignettes=FALSE)
-knitr::opts_chunk$set(
-collapse = TRUE,
-comment = "#>"
-)
-library(dplyr)
-library(stuart)
-annot_mini <- read.csv(url("https://raw.githubusercontent.com/kbroman/MUGAarrays/master/UWisc/mini_uwisc_v2.csv"))
-data(genos)
-summary(genos)
-data(phenos)
-summary(phenos)
-strains <- geno_strains(ref=annot_mini,geno=genos,par1=c("StrainsA_1","StrainsA_2"),par2=c("StrainsB_1","StrainsB_2"),name1="parent1",name2="parent2")
-head(strains)
-genos <- genos %>% filter(!Sample.ID %in% c("StrainsA_1", "StrainsA_2", "StrainsB_1","StrainsB_2"))
-data(stuart_tab)
-summary(stuart_tab)
-tab2 <- mark_match(stuart_tab,ref=strains)
-tab2 %>% filter(exclude_match==1)
-tab2 <- mark_poly(tab2)
-head(tab2)
-tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
-head(tab2)
-knitr::opts_chunk$set(
-collapse = TRUE,
-comment = "#>"
-)
-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)
-genos <- genos %>% filter(!Sample.ID %in% c("StrainsA_1", "StrainsA_2", "StrainsB_1","StrainsB_2"))
-data(stuart_tab)
-summary(stuart_tab)
-View(stuart_tab)
-tab2 <- mark_match(stuart_tab,ref=strains)
-tab2 %>% filter(exclude_match==1)
-View(tab2)
-tab2 <- mark_poly(tab2)
-head(tab2)
-View(tab2)
-tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
-View(tab2)
-library(stuart)
-knitr::opts_chunk$set(
-collapse = TRUE,
-comment = "#>"
-)
-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)
-genos <- genos %>% filter(!Sample.ID %in% c("StrainsA_1", "StrainsA_2", "StrainsB_1","StrainsB_2"))
-data(stuart_tab)
-summary(stuart_tab)
-tab2 <- mark_match(stuart_tab,ref=strains)
-tab2 %>% filter(exclude_match==1)
-tab2 <- mark_poly(tab2)
-head(tab2)
-tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
-head(tab2)
-View(tab2)
-tab2 <- mark_allele(tab=tab2,ref=strains,par1="parent1",par2="parent2")
-tab2 %>% arrange(desc(exclude_allele)) %>% head()
-strains %>% filter(marker %in% c("gJAX00038569","gJAX00425031","gUNC12245354","gUNC15530876","gUNC21555204","gUNC21596600")) %>% arrange(marker) %>% select(marker,parent1,parent2)
-View(tab2)
-strains %>% filter(marker %in% c("gJAX00038569","gJAX00425031","gUNC12245354","gUNC15530876","gUNC21555204","gUNC21596600")) %>% arrange(marker) %>% select(marker,parent1,parent2)
-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]
-devtools::build_vignettes()
-devtools::build_manual()
-build_manual
-devtools::build_manual
-Rd2pdf
-tools::texi2pdf
-devtools::build_manual()
-devtools::build(path=".",vignettes=FALSE,manual=TRUE)
-devtools::build_manual()
-Rd2pdf()
-Rd2pdf
-install.packages("RdUtils")
-RdUtils
-RdUtils()
-system("R CMD Rd2pdf stuart")
-system("R CMD Rd2pdf stuaRt")
-getwd()
-cd ..
-setwd("~/Documents/stuart_package/stuart")
-setwd("~/Documents/stuart_package/stuart")
-setwd("~/Documents/stuart_package")
-system("R CMD Rd2pdf stuaRt")
-system("R CMD Rd2pdf stuart")
-system("R CMD Rd2pdf stuart")
-setwd("~/Documents/stuart_package/stuart")
-devtools::build_manual()
-getwd()
-devtools::build_manual(path=".")
-devtools::build_manual(path=".")
-View(genos)
-devtools::build(path=".",vignettes=FALSE)
-devtools::build_vignettes()
-devtools::build_manual(path=".")
-devtools::build_manual(path=".")
-devtools::build(path=".",vignettes=FALSE)
-devtools::build_manual(path=".")
-roxygen2::roxygenise()
-devtools::build_manual(path=".")
-library(dplyr)
-library(stuart)
-test <- tibble(x=c("A","T"),y=c("A","A"),z=c("A","A"))
-View(test)
-View(test)
-View(test)
-View(test)
-View(rqtl_file)
-View(annot_mini)
-View(genos)
-View(genos)
-View(genos)
-View(test)
-library(dplyr)
-library(stuart)
-test <- tibble(x=c("A","T"),y=c("A","A"),z=c("A","A"))
-View(test)
-test <- test %>% mutate(geno=x)
-View(test)
-test %>% mutate(geno = ifelse(geno==y,geno,"N"))
-test <- test %>% mutate(geno = ifelse(geno==y,geno,"N"))
-test <- test %>% mutate(geno = ifelse(geno==z,geno,"N"))
-View(test)
-test <- tibble(x=c("A","T"),y=c("A","A"),z=c("A","N"))
-test <- tibble(x=c("A","T"),y=c("A","A"),z=c("A","N"))
-test <- test %>% mutate(geno=x)
-print(test)
-test <- test %>% mutate(geno = ifelse(geno==y,geno,"N"))
-print(test)
-test <- test %>% mutate(geno = ifelse(geno==z,geno,"N"))
-print(test)
-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)