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Relatedness.R
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#-------------------------------------------------------------------------------------------#
# Author : Andrew J Skelton |
# Language : R Statistical Programming Language |
# Study : WES PID |
# Data Owner : Newcastle University - Prof. Sophie Hambleton |
# Description : Check expected relatedness between samples, against a relatedness |
# coefficient. Statistic is ~1 for a sample compared to itself. |
# Method : Yang et al, Nature Genetics 2010 |
#-------------------------------------------------------------------------------------------#
##'Set the Working Directory, load essential packages
##'-----------------------------------------------------------------------------------------#
library(dplyr)
library(readr)
library(openxlsx)
foo <- read_tsv("/Volumes/andrew/Temp/Raw_Callset/out.relatedness2") %>%
as.data.frame
ped <- read_tsv("/Volumes/WORKING_DATA/Exome_Project/Scripts/Ref/Samples.ped", col_names=F) %>%
as.data.frame
##'-----------------------------------------------------------------------------------------#
##' Search for expected vs unexpected relatedness
##
##'-----------------------------------------------------------------------------------------#
Output_Table <- c()
for(i in unique(ped$X1)) {
FAM_in <- i
ped_in <- ped %>% filter(X1 == FAM_in)
foo_in <- foo %>% filter(INDV1 %in% ped_in$X2)
foo_r <- foo %>% filter(INDV1 %in% ped_in$X2, INDV2 %in% ped_in$X2)
foo_nr <- foo %>% filter(!(INDV1 %in% ped_in$X2), !(INDV2 %in% ped_in$X2))
out <- c()
for(j in 1:nrow(ped_in)) {
sampl <- ped_in[j,2]
temp1 <- foo_r %>% filter(INDV1 == sampl, INDV2 == sampl)
self <- ifelse(temp1$RELATEDNESS_AJK > 0.95,"Sample OK Within Itself","Possible Sample Problem")
out <- bind_rows(out,
data.frame(FAM_ID = FAM_in,
Indv1 = temp1$INDV1, Indv2 = temp1$INDV2,
R_AJK = temp1$RELATEDNESS_AJK,
Call = self,
Relationship = "Self"))
temp2 <- foo_r %>% filter(INDV1 == sampl, INDV2 != sampl)
if(nrow(temp2) > 0) {
for(k in 1:nrow(temp2)) {
self <- ifelse(temp2[k,]$RELATEDNESS_AJK > 0.2,"Samples Likely Related","Samples Likely Unrelated")
subped <- ped %>% filter(X2 == temp2[k,]$INDV1 | X2 == temp2[k,]$INDV2)
if((subped$X3[1] == subped$X3[2]) & subped$X3[1] != 0) {
rela <- "Siblings"
}else if((subped$X4[1] == subped$X4[2]) & subped$X4[1] != 0) {
rela <- "Siblings"
}else if(c(subped$X3,subped$X4) %>% table %>% .[["0"]] == 4){
rela <- "Parent-Parent"
}else if(subped$X3 %>% table %>% .[["0"]] == 1){
rela <- "Parent-Child"
}else if(subped$X4 %>% table %>% .[["0"]] == 1){
rela <- "Parent-Child"
}else {
rela <- "Other"
}
# ifelse(subped$X3 %>% table %>% .[["0"]] == 1, "Parent-Child","Other")
# ifelse(subped$X4 %>% table %>% .[["0"]] == 1, "Parent-Child","Other")
# ifelse(c(subped$X3,subped$X4) %>% table %>% .[["0"]] == 4, "Parent-Parent","Other")
# ifelse(c(subped$X3,subped$X4) %>% table %>% .[["0"]] == 4, "Parent-Parent","Other")
out <- bind_rows(out,
data.frame(FAM_ID = FAM_in,
Indv1 = temp2[k,]$INDV1, Indv2 = temp2[k,]$INDV2,
R_AJK = temp2[k,]$RELATEDNESS_AJK,
Call = self,
Relationship = rela))
}
}
}
Output_Table <- bind_rows(Output_Table,out)
message(i)
}
wb <- openxlsx::createWorkbook()
openxlsx::addWorksheet(wb, "Sample-Sample_Checks")
OT_1 <- Output_Table %>% as.data.frame %>% filter(Relationship == "Self")
openxlsx::writeData(wb, "Sample-Sample_Checks", OT_1)
openxlsx::addWorksheet(wb, "Parent-Parent")
OT_2 <- Output_Table %>% as.data.frame %>% filter(Relationship == "Parent-Parent")
openxlsx::writeData(wb, "Parent-Parent", OT_2)
openxlsx::addWorksheet(wb, "Siblings")
OT_3 <- Output_Table %>% as.data.frame %>% filter(Relationship == "Siblings")
openxlsx::writeData(wb, "Siblings", OT_3)
openxlsx::addWorksheet(wb, "Parent-Child")
OT_4 <- Output_Table %>% as.data.frame %>% filter(Relationship == "Parent-Child")
openxlsx::writeData(wb, "Parent-Child", OT_4)
openxlsx::saveWorkbook(wb, "/Volumes/WORKING_DATA/Exome_Project/Preprocessing/Relatedness.xlsx", overwrite = T)
foo <- read_tsv("/Volumes/andrew/2016Jun_WES_Karin/Recalibrated_Callset/out.relatedness2") %>% as.data.frame
ped <- read_tsv("/Volumes/andrew/2016Jun_WES_Karin/pedigree/Samples.ped", col_names = F) %>% as.data.frame
Output_Table <- c()
for(i in unique(ped$X1)) {
FAM_in <- i
ped_in <- ped %>% filter(X1 == FAM_in)
foo_in <- foo %>% filter(INDV1 %in% ped_in$X2)
foo_r <- foo %>% filter(INDV1 %in% ped_in$X2, INDV2 %in% ped_in$X2)
foo_nr <- foo %>% filter(!(INDV1 %in% ped_in$X2), !(INDV2 %in% ped_in$X2))
out <- c()
for(j in 1:nrow(ped_in)) {
sampl <- ped_in[j,2]
temp1 <- foo_r %>% filter(INDV1 == sampl, INDV2 == sampl)
self <- ifelse(temp1$RELATEDNESS_PHI > 0.95,"Sample OK Within Itself","Possible Sample Problem")
out <- bind_rows(out,
data.frame(FAM_ID = FAM_in,
Indv1 = temp1$INDV1, Indv2 = temp1$INDV2,
R_AJK = temp1$RELATEDNESS_PHI,
Call = self,
Relationship = "Self"))
temp2 <- foo_r %>% filter(INDV1 == sampl, INDV2 != sampl)
if(nrow(temp2) > 0) {
for(k in 1:nrow(temp2)) {
self <- ifelse(temp2[k,]$RELATEDNESS_PHI > 0.2,"Samples Likely Related","Samples Likely Unrelated")
subped <- ped %>% filter(X2 == temp2[k,]$INDV1 | X2 == temp2[k,]$INDV2)
if((subped$X3[1] == subped$X3[2]) & subped$X3[1] != 0) {
rela <- "Siblings"
}else if((subped$X4[1] == subped$X4[2]) & subped$X4[1] != 0) {
rela <- "Siblings"
}else if(c(subped$X3,subped$X4) %>% table %>% .[["0"]] == 4){
rela <- "Parent-Parent"
}else if(subped$X3 %>% table %>% .[["0"]] == 1){
rela <- "Parent-Child"
}else if(subped$X4 %>% table %>% .[["0"]] == 1){
rela <- "Parent-Child"
}else {
rela <- "Other"
}
# ifelse(subped$X3 %>% table %>% .[["0"]] == 1, "Parent-Child","Other")
# ifelse(subped$X4 %>% table %>% .[["0"]] == 1, "Parent-Child","Other")
# ifelse(c(subped$X3,subped$X4) %>% table %>% .[["0"]] == 4, "Parent-Parent","Other")
# ifelse(c(subped$X3,subped$X4) %>% table %>% .[["0"]] == 4, "Parent-Parent","Other")
out <- bind_rows(out,
data.frame(FAM_ID = FAM_in,
Indv1 = temp2[k,]$INDV1, Indv2 = temp2[k,]$INDV2,
R_AJK = temp2[k,]$RELATEDNESS_PHI,
Call = self,
Relationship = rela))
}
}
}
Output_Table <- bind_rows(Output_Table,out)
message(i)
}
# wb <- openxlsx::createWorkbook()
# openxlsx::addWorksheet(wb, "Sample-Sample_Checks")
OT_1 <- Output_Table %>% as.data.frame %>% filter(Relationship == "Self")
# openxlsx::writeData(wb, "Sample-Sample_Checks", OT_1)
# openxlsx::addWorksheet(wb, "Parent-Parent")
OT_2 <- Output_Table %>% as.data.frame %>% filter(Relationship == "Parent-Parent")
# openxlsx::writeData(wb, "Parent-Parent", OT_2)
# openxlsx::addWorksheet(wb, "Siblings")
OT_3 <- Output_Table %>% as.data.frame %>% filter(Relationship == "Siblings")
# openxlsx::writeData(wb, "Siblings", OT_3)
# openxlsx::addWorksheet(wb, "Parent-Child")
OT_4 <- Output_Table %>% as.data.frame %>% filter(Relationship == "Parent-Child")
# openxlsx::writeData(wb, "Parent-Child", OT_4)
# openxlsx::saveWorkbook(wb, "/Volumes/WORKING_DATA/Exome_Project/Preprocessing/Relatedness.xlsx", overwrite = T)