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Commit 070023a0 authored by mariefbourdon's avatar mariefbourdon
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modif tab_mark to add chr and pos

parent 1367ad7d
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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"))
data(stuart_tab)
summary(stuart_tab)
tab2 <- mark_match(stuart_tab,ref=strains)
tab2 %>% filter(exclude_match==1) %>% print.data.frame()
tab2 <- mark_poly(tab2)
head(tab2) %>% print.data.frame()
tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
head(tab2) %>% print.data.frame()
tab2 <- mark_allele(tab=tab2,ref=strains,par1="parent1",par2="parent2")
tab2 %>% arrange(desc(exclude_allele)) %>% head() %>% print.data.frame()
strains %>% filter(marker %in% c("gJAX00038569","gJAX00425031","gUNC12245354",
"gUNC15530876","gUNC21555204","gUNC21596600")) %>% arrange(marker) %>%
select(marker,parent1,parent2) %>% print.data.frame()
rqtl_file <- write_rqtl(geno=genos,pheno=phenos,tab=tab2,
ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox",path = "rqtl_file.csv")
rqtl_file[1:10,1:7] %>% print.data.frame()
bad_markers <- mark_estmap(map=newmap_after,dist=100)
tab2 %>% filter(marker %in% c("S6J010381992","S6J205609960"))
View(annot_mini)
annot_mini %>% filter(marker %in% c("S6J010381992","S6J205609960"))
# annot_mini %>% filter(marker %in% bad_markers)
View(annot_mini)
View(strains)
strains %>% filter(marker %in% c("S6J010381992","S6J205609960"))
data(stuart_cross)
devtools::build(path=".",vignettes=FALSE)
devtools::build_vignettes()
devtools::build_manual(path=".")
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(dplyr)
library(stuart)
annot_mini <- read.csv(url("https://raw.githubusercontent.com/kbroman/MUGAarrays/master/UWisc/mini_uwisc_v2.csv"))
data(genos)
summary(genos)
data(phenos)
summary(phenos)
strains <- geno_strains(ref=annot_mini,geno=genos,par1=c("StrainsA_1","StrainsA_2"),
par2=c("StrainsB_1","StrainsB_2"),name1="parent1",name2="parent2")
head(strains) %>% print.data.frame()
genos <- genos %>% filter(!Sample.ID %in% c("StrainsA_1", "StrainsA_2",
"StrainsB_1","StrainsB_2"))
data(stuart_tab)
summary(stuart_tab)
tab2 <- mark_match(stuart_tab,ref=strains)
tab2 %>% filter(exclude_match==1) %>% print.data.frame()
tab2 <- mark_poly(tab2)
head(tab2) %>% print.data.frame()
tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
head(tab2) %>% print.data.frame()
mark_prop(tab2,cross="F2",pval=0.05) %>% head() %>% print.data.frame()
a <- mark_prop(tab2,cross="F2",pval=0.05)
View(tab2)
View(a)
identical(a,tab2)
library(stuart)
devtools::build(path=".",vignettes=FALSE)
devtools::build_vignettes()
devtools::build_manual(path=".")
library(stuart)
devtools::build_vignettes()
test <- tibble(sample.id=c(1,2,3),pheno=c(4,5,6))
library(dplyr)
library(dplyr)
test <- tibble(sample.id=c(1,2,3),pheno=c(4,5,6))
View(test)
test %>% rename(1="id")
test %>% rename("id"=1)
library(dplyr)
library(stuart)
write_rqtl <- function(geno,pheno,tab,ref,par1,par2,par_N=TRUE,prefix,pos,path=NA){
#create geno column in geno df
geno <- geno %>% unite(Geno,c("allele_1","allele_2"),sep="",remove=FALSE)
#recode genotypes to have all heterozygous encoded the same way (ex: only "AT", no "TA")
geno <- geno %>% mutate(Geno=recode(Geno,
"TA" = "AT",
"GA" = "AG",
"CA" = "AC",
"GT" = "TG",
"CT" = "TC",
"GC" = "CG"))
#create df with counts for each genotype
df_count <- tibble(marker = as.character(unique(geno$marker)),
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$marker){
#extract alleles for each marker
Alleles <- geno %>% filter(marker==i) %>%
select(c(marker,id,Geno,allele_1,allele_2)) %>%
pivot_longer(c(allele_1,allele_2),names_to="Allele_name",values_to="Allele") %>%
distinct(Allele) %>% filter(Allele != "-")
Alleles <- as.factor(paste(Alleles$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(marker == i,
paste(Alleles[1]), allele_1))
#count for homozygous for allele 1
n1 <- geno %>% filter(marker==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(marker == i,
n1$n, n_HM1))
}
#if marker not polymorphic
if(is.na(Alleles[2])==TRUE){
#NA as allele_2
df_count <- df_count %>% mutate(allele_2 = ifelse(marker == i,
NA, allele_2))
#NA as n_HM2
df_count <- df_count %>% mutate(n_HM2 = ifelse(marker == i,
NA, n_HM2))
#NA as n_HT
df_count <- df_count %>% mutate(n_HT = ifelse(marker == i,
NA, n_HT))
} else {
#add alleles to df_count
df_count <- df_count %>% mutate(allele_2 = ifelse(marker == i,
paste(Alleles[2]), allele_2))
#count for homozygous for allele 2
n2 <- geno %>% filter(marker==i) %>%
filter(Geno == paste(Alleles[2],Alleles[2],sep="")) %>%
summarise(n=n())
#add count for homozygous for allele 1 to df_count
df_count <- df_count %>% mutate(n_HM2 = ifelse(marker == i,
n2$n, n_HM2))
#count for heterozygous
n3 <- geno %>% filter(marker==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(marker == i,
n3$n, n_HT))
}
#count for NA
n4 <- geno %>% filter(marker==i) %>%
filter(Geno == "--" |
Geno == paste(Alleles[1],"-",sep="") | Geno == paste(Alleles[2],"-",sep="") |
Geno == paste("-",Alleles[1],sep="") | Geno == paste("-",Alleles[2],sep="")) %>%
summarise(n=n())
#add count for NA to df_count
df_count <- df_count %>% mutate(n_NA = ifelse(marker == i,
n4$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))
#save useful columns in annot dataframe
annot <- annot %>% select(marker,chr,!!sym(pos))
print(annot)
#return
return(df_count)
}
tab_mark(genos,annot_mini,"cM_cox")
library(tidyr)
tab_mark(genos,annot_mini,"cM_cox")
tab_mark <- function(geno,annot,pos){
#rename df columns
geno <- geno %>% rename("marker"=1,
"id"=2,
"allele_1"=3,
"allele_2"=4)
#extract snps non excluded
if("exclude_match" %in% colnames(tab)){
tab <- tab %>% filter(exclude_match==0)
#create geno column in geno df
geno <- geno %>% unite(Geno,c("allele_1","allele_2"),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(marker = as.character(unique(geno$marker)),
allele_1 = NA,
allele_2 = NA,
n_HM1 = NA,
n_HM2 = NA,
n_HT = NA,
n_NA = NA)
## loop to count genotype
for(i in df_count$marker){
#extract alleles for each marker
Alleles <- geno %>% filter(marker==i) %>%
select(c(marker,id,Geno,allele_1,allele_2)) %>%
pivot_longer(c(allele_1,allele_2),names_to="Allele_name",values_to="Allele") %>%
distinct(Allele) %>% filter(Allele != "-")
Alleles <- as.factor(paste(Alleles$Allele))
#sort alleles
Alleles <- factor(Alleles,levels=c("A","T","C","G"))
Alleles <- sort(Alleles)
#add alleles and counts, only for markers with alleles (not markers with no genotyped ind)
if(all(rapportools::is.empty(Alleles))==FALSE){
#add alleles to df_count
df_count <- df_count %>% mutate(allele_1 = ifelse(marker == i,
paste(Alleles[1]), allele_1))
#count for homozygous for allele 1
n1 <- geno %>% filter(marker==i) %>%
filter(Geno == paste(Alleles[1],Alleles[1],sep="")) %>%
summarise(n=n())
#add count for homozygous for allele 1 to df_count
df_count <- df_count %>% mutate(n_HM1 = ifelse(marker == i,
n1$n, n_HM1))
}
if("exclude_poly" %in% colnames(tab)){
tab <- tab %>% filter(exclude_poly==0)
#if marker not polymorphic
if(is.na(Alleles[2])==TRUE){
#NA as allele_2
df_count <- df_count %>% mutate(allele_2 = ifelse(marker == i,
NA, allele_2))
#NA as n_HM2
df_count <- df_count %>% mutate(n_HM2 = ifelse(marker == i,
NA, n_HM2))
#NA as n_HT
df_count <- df_count %>% mutate(n_HT = ifelse(marker == i,
NA, n_HT))
} else {
#add alleles to df_count
df_count <- df_count %>% mutate(allele_2 = ifelse(marker == i,
paste(Alleles[2]), allele_2))
#count for homozygous for allele 2
n2 <- geno %>% filter(marker==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(marker == i,
n2$n, n_HM2))
#count for heterozygous
n3 <- geno %>% filter(marker==i) %>%
filter(Geno == paste(Alleles[1],Alleles[2],sep="")) %>%
summarise(n=n())
#add count for homozygous for allele 1 to df_count
df_count <- df_count %>% mutate(n_HT = ifelse(marker == i,
n3$n, n_HT))
}
if("exclude_prop" %in% colnames(tab)){
tab <- tab %>% filter(exclude_prop==0)
#count for NA
n4 <- geno %>% filter(marker==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(marker == i,
n4$n, n_NA))
}
if("exclude_allele" %in% colnames(tab)){
tab <- tab %>% filter(exclude_allele==0)
#change class of counts as numeric :
df_count$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$n_NA %>% as.numeric()
#add 0 for null counts
df_count <- df_count %>% mutate_at(.vars=vars(n_HM1,n_HM2,n_HT,n_NA),~replace(., is.na(.), 0))
#save useful columns in annot dataframe
annot <- annot %>% select(marker,chr,!!sym(pos))
tab <- left_join(tab,annot)
#return
return(df_count)
}
#filter genotypes for non excluded markers in geno file
geno <- geno %>% select(c(marker,id,allele_1,allele_2)) %>% filter(marker %in% tab$marker)
#recode parents' names to match column names nomenclature
par1 <- make.names(par1)
par2 <- make.names(par2)
#keep parental lines genotypes
colnames(ref) <- make.names(colnames(ref))
ref <- ref %>% select(marker,chr,!!sym(pos),!!sym(par1),!!sym(par2))
#merge genotypes with parents
geno <- left_join(geno,ref,by=c("marker"="marker"))
#remove snps with no position
geno <- geno %>% filter(is.na(chr)==FALSE) %>% filter(is.na(!!sym(pos))==FALSE)
#recode "-" in "N" in geno file
geno <- geno %>% mutate(allele_1 = recode(allele_1,
"-" = "N"))
geno <- geno %>% mutate(allele_2 = recode(allele_2,
"-" = "N"))
#recode geno in factors with same levels
geno <- geno %>% mutate(allele_1 = factor(allele_1,levels=c("A","C","G","H","N","T")))
geno <- geno %>% mutate(allele_2 = factor(allele_2,levels=c("A","C","G","H","N","T")))
#recode genotypes depending on parents' genotypes
geno <- geno %>% mutate(Geno = case_when(
#if one allele not genotyped:
allele_1=="N" | allele_2=="N" ~ "NA",
#if both alleles genotyped
##homozygous 0
allele_1==allele_2 & allele_1==!!sym(par1) ~ "0",
##homozygous 2
allele_1==allele_2 & allele_1==!!sym(par2) ~ "2",
##heterozygous
allele_1!=allele_2 ~ "1",
#if parental strains are N/H
##homozygous for parent that is N/H
###homozygous 0
(!!sym(par1)%in%c("H","N") | !!sym(par2)%in%c("H","N")) &
!!sym(par1)%in%c("H","N") ~ "0",
###homozygous 2
(!!sym(par1)%in%c("H","N") | !!sym(par2)%in%c("H","N")) &
!!sym(par2)%in%c("H","N") ~ "2"
)
)
#keep positions of markers
markers <- geno %>% select(marker,chr,!!sym(pos)) %>% distinct()
markers <- markers %>% arrange(chr,!!sym(pos))
#keep only interesting columns in geno file
geno <- geno %>% arrange(chr,!!sym(pos))
geno <- geno %>% select(marker,id,Geno)
#remove prefix
geno <- geno %>% mutate(id=str_remove(id,prefix))
#keep only non excluded markers and merge with positions
markers <- markers %>% mutate(marker=as.character(marker))
markers <- markers %>% mutate(chr=as.character(chr))
geno <- markers %>% select(marker,chr,!!sym(pos)) %>% full_join(.,geno,by="marker")
#pivoting
geno <- geno %>% pivot_wider(names_from = c(marker,chr,!!sym(pos)),values_from = Geno,names_sep=",")
geno <- geno %>% mutate(id=as.character(id))
geno <- geno %>% rename("id,,"=id)
#merge with phenotype file
pheno <- pheno %>% rename("id"=1)
pheno <- pheno %>% mutate_all(as.character)
colnames(pheno) <- str_c(colnames(pheno),",,")
qtl_file <- right_join(pheno,geno,by=c("id,,"="id,,"))
#prepare file
qtl_file <- rbind(colnames(qtl_file),qtl_file)
qtl_file <- separate_rows(qtl_file,everything(),sep=",")
colnames(qtl_file) <- qtl_file[1,]
qtl_file <- qtl_file %>% slice(-1)
if(is.na(path)==FALSE){
write.csv(qtl_file,file=path,quote=FALSE,row.names = FALSE)
tab_mark(genos,annot_mini,"cM_cox")
tab_mark <- function(geno,annot,pos){
#rename df columns
geno <- geno %>% rename("marker"=1,
"id"=2,
"allele_1"=3,
"allele_2"=4)
#create geno column in geno df
geno <- geno %>% unite(Geno,c("allele_1","allele_2"),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
tab <- tibble(marker = as.character(unique(geno$marker)),
allele_1 = NA,
allele_2 = NA,
n_HM1 = NA,
n_HM2 = NA,
n_HT = NA,
n_NA = NA)
## loop to count genotype
for(i in tab$marker){
#extract alleles for each marker
Alleles <- geno %>% filter(marker==i) %>%
select(c(marker,id,Geno,allele_1,allele_2)) %>%
pivot_longer(c(allele_1,allele_2),names_to="Allele_name",values_to="Allele") %>%
distinct(Allele) %>% filter(Allele != "-")
Alleles <- as.factor(paste(Alleles$Allele))
#sort alleles
Alleles <- factor(Alleles,levels=c("A","T","C","G"))
Alleles <- sort(Alleles)
#add alleles and counts, only for markers with alleles (not markers with no genotyped ind)
if(all(rapportools::is.empty(Alleles))==FALSE){
#add alleles to tab
tab <- tab %>% mutate(allele_1 = ifelse(marker == i,
paste(Alleles[1]), allele_1))
#count for homozygous for allele 1
n1 <- geno %>% filter(marker==i) %>%
filter(Geno == paste(Alleles[1],Alleles[1],sep="")) %>%
summarise(n=n())
#add count for homozygous for allele 1 to tab
tab <- tab %>% mutate(n_HM1 = ifelse(marker == i,
n1$n, n_HM1))
}
return(qtl_file)
#if marker not polymorphic
if(is.na(Alleles[2])==TRUE){
#NA as allele_2
tab <- tab %>% mutate(allele_2 = ifelse(marker == i,
NA, allele_2))
#NA as n_HM2
tab <- tab %>% mutate(n_HM2 = ifelse(marker == i,
NA, n_HM2))
#NA as n_HT
tab <- tab %>% mutate(n_HT = ifelse(marker == i,
NA, n_HT))
} else {
#add alleles to tab
tab <- tab %>% mutate(allele_2 = ifelse(marker == i,
paste(Alleles[2]), allele_2))
#count for homozygous for allele 2
n2 <- geno %>% filter(marker==i) %>%
filter(Geno == paste(Alleles[2],Alleles[2],sep="")) %>%
summarise(n=n())
#add count for homozygous for allele 1 to tab
tab <- tab %>% mutate(n_HM2 = ifelse(marker == i,
n2$n, n_HM2))
#count for heterozygous
n3 <- geno %>% filter(marker==i) %>%
filter(Geno == paste(Alleles[1],Alleles[2],sep="")) %>%
summarise(n=n())
#add count for homozygous for allele 1 to tab
tab <- tab %>% mutate(n_HT = ifelse(marker == i,
n3$n, n_HT))
}
data(phenos)
summary(phenos)
View(phenos)
pheno %>% rename("sample"="Ind")
phenos %>% rename("sample"="Ind")
phenos <- pheno %>% rename("sample"="Ind")
phenos <- phenos %>% rename("sample"="Ind")
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) %>% print.data.frame()
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) %>% print.data.frame()
tab2 <- mark_poly(tab2)
head(tab2) %>% print.data.frame()
tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
head(tab2) %>% print.data.frame()
mark_prop(tab2,cross="F2",pval=0.05) %>% head() %>% print.data.frame()
tab2 <- mark_allele(tab=tab2,ref=strains,par1="parent1",par2="parent2")
tab2 %>% arrange(desc(exclude_allele)) %>% head() %>% print.data.frame()
strains %>% filter(marker %in% c("gJAX00038569","gJAX00425031","gUNC12245354",
"gUNC15530876","gUNC21555204","gUNC21596600")) %>% arrange(marker) %>%
select(marker,parent1,parent2) %>% print.data.frame()
rqtl_file <- write_rqtl(geno=genos,pheno=phenos,tab=tab2,
ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox")
library(dplyr)
library(stuart)
rqtl_file <- write_rqtl(geno=genos,pheno=phenos,tab=tab2,
ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox")
library(stuart)
library(dplyr)
library(stuart)
rqtl_file <- write_rqtl(geno=genos,pheno=phenos,tab=tab2,
ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox")
rqtl_file <- write_rqtl(geno=genos,pheno=phenos,tab=tab2,
ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox")
library(stuart)
library(stringr)
rqtl_file <- write_rqtl(geno=genos,pheno=phenos,tab=tab2,
ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox")
detach("package:stuart", unload = TRUE)
install.packages(stuart)
library(tidyverse)
rqtl_file <- write_rqtl(geno=genos,pheno=phenos,tab=tab2,
ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox")
write_rqtl(geno=genos,pheno=phenos,tab=tab2,
ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox")
detach("package:stringr", unload = TRUE)
detach("package:tibble", unload = TRUE)
detach("package:tidyr", unload = TRUE)
detach("package:tidyverse", unload = TRUE)
detach("package:readr", unload = TRUE)
detach("package:purrr", unload = TRUE)
detach("package:forcats", unload = TRUE)
detach("package:ggplot2", unload = TRUE)
detach("package:dplyr", unload = TRUE)
devtools::build(path=".",vignettes=FALSE)
devtools::build_vignettes()
devtools::build_manual(as.package())
devtools::build_manual(
)
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) %>% 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)
tab2 <- mark_match(stuart_tab,ref=strains)
tab2 %>% filter(exclude_match==1) %>% print.data.frame()
tab2 <- mark_poly(tab2)
head(tab2) %>% print.data.frame()
tab2 <- mark_prop(tab2,cross="F2",homo=0.1,hetero=0.1)
head(tab2) %>% print.data.frame()
mark_prop(tab2,cross="F2",pval=0.05) %>% head() %>% print.data.frame()
tab2 <- mark_allele(tab=tab2,ref=strains,par1="parent1",par2="parent2")
tab2 %>% arrange(desc(exclude_allele)) %>% head() %>% print.data.frame()
strains %>% filter(marker %in% c("gJAX00038569","gJAX00425031","gUNC12245354",
"gUNC15530876","gUNC21555204","gUNC21596600")) %>% arrange(marker) %>%
select(marker,parent1,parent2) %>% print.data.frame()
stuart_cross <- write_rqtl(geno=genos,pheno=phenos,tab=tab2,
ref=strains,par1="parent1",par2="parent2",prefix="ind_",pos="cM_cox")
stuart_cross[1:10,1:7] %>% print.data.frame()
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) %>% 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)