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updated pnca_extraction and AF_OR calcs

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Tanushree Tunstall 2020-03-23 17:36:42 +00:00
parent eb021349fe
commit b331227023
4 changed files with 195 additions and 699 deletions
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# run glm model
model = glm(y ~ x, family = binomial)
#model = glm(y ~ x, family = binomial(link = "logit"))
summary(model)
#**********
# extract relevant model output
#**********
# extract log OR i.e the Beta estimate of the logistic model for a given snp
my_logor = summary(model)$coefficients[2,1]
print(paste0('Beta:', my_logor))
# extract SE of the logistic model for a given snp
my_se = summary(model)$coefficients[2,2]
print(paste0('SE:', my_se))
# extract Z of the logistic model for a given snp
my_zval = summary(model)$coefficients[2,3]
print(paste0('Z-value:', my_zval))
# Dervive OR i.e exp(my_logor) from the logistic model for a given snp
#my_or = round(exp(summary(model)$coefficients[2,1]), roundto)
my_or = exp(summary(model)$coefficients[2,1])
print(paste0('OR:', my_or))
# sanity check : should be True
log(my_or) == my_logor
# extract P-value of the logistic model for a given snp
my_pval = summary(model)$coefficients[2,4]
print(paste0('P-value:', my_pval))
# extract confint interval of snp (2 steps, since the output is a named number)
ci_mod = exp(confint(model))[2,]
my_ci = paste(ci_mod[["2.5 %"]], ",", ci_mod[["97.5 %"]])
print(paste0('CI:', my_ci))
#*************
# Assign the regression output in the original df
# you can use ('=' or '<-/->')
#*************
#pnca_snps_or$logistic_logOR[pnca_snps_or$Mutationinformation == i] = my_logor
my_logor -> pnca_snps_or$logistic_logOR[pnca_snps_or$Mutationinformation == i]
my_logor
pnca_snps_or$Mutationinformation == i
View(pnca_snps_or)
#===============
# Step 4: Calculate for one snp
# using i, when you run the loop, it is easy
#===============
i = "pnca_p.trp68gly"
pnca_snps_or = read.csv("../Data_original/pnca_snps_for_or_calcs.csv"
, stringsAsFactors = F
, header = T) #2133
# uncomment as necessary
pnca_snps_or = pnca_snps_or[1:5,]
pnca_snps_or = pnca_snps_or[c(1:5),]
#===============
pnca_snps_or = read.csv("../Data_original/pnca_snps_for_or_calcs.csv"
, stringsAsFactors = F
, header = T) #2133
pnca_snps_or = pnca_snps_or[1:5,]
pnca_snps_or = pnca_snps_or[c(1:5),]
pnca_snps_or = pnca_snps_or[1:5]
pnca_snps_or = read.csv("../Data_original/pnca_snps_for_or_calcs.csv"
, stringsAsFactors = F
, header = T) #2133
pnca_snps_or = pnca_snps_or[1:5]
pnca_snps_or = read.csv("../Data_original/pnca_snps_for_or_calcs.csv"
, stringsAsFactors = F
, header = T) #2133
foo = pnca_snps_or[c(1:5,)]
foo = pnca_snps_or[c(1:5),]
foo = as.data.frame(pnca_snps_or[c(1:5),])
View(foo)
# create an empty dataframe
pnca_snps_or = as.data.frame(pnca_snps_or[c(1:5),])
# IV: corresponds to each unique snp (extracted using grep)
x = as.numeric(grepl(i,raw_data$all_muts_pza))
# DV: pyrazinamide 0 or 1
y = as.numeric(raw_data$pyrazinamide)
table(y,x)
# run glm model
model = glm(y ~ x, family = binomial)
#model = glm(y ~ x, family = binomial(link = "logit"))
summary(model)
my_logor = summary(model)$coefficients[2,1]
print(paste0('Beta:', my_logor))
# extract SE of the logistic model for a given snp
my_se = summary(model)$coefficients[2,2]
print(paste0('SE:', my_se))
# extract Z of the logistic model for a given snp
my_zval = summary(model)$coefficients[2,3]
print(paste0('Z-value:', my_zval))
# Dervive OR i.e exp(my_logor) from the logistic model for a given snp
#my_or = round(exp(summary(model)$coefficients[2,1]), roundto)
my_or = exp(summary(model)$coefficients[2,1])
print(paste0('OR:', my_or))
# sanity check : should be True
log(my_or) == my_logor
# extract P-value of the logistic model for a given snp
my_pval = summary(model)$coefficients[2,4]
print(paste0('P-value:', my_pval))
# extract confint interval of snp (2 steps, since the output is a named number)
ci_mod = exp(confint(model))[2,]
my_ci = paste(ci_mod[["2.5 %"]], ",", ci_mod[["97.5 %"]])
print(paste0('CI:', my_ci))
#*************
# Assign the regression output in the original df
# you can use ('=' or '<-/->')
#*************
#pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i] = my_logor
my_logor -> pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i]
my_or -> pnca_snps_or$OR[pnca_snps_or$mutation == i]
my_pval -> pnca_snps_or$pvalue[pnca_snps_or$mutation == i]
my_zval -> pnca_snps_or$zvalue[pnca_snps_or$mutation == i]
my_se -> pnca_snps_or$logistic_se[pnca_snps_or$mutation == i]
my_ci -> pnca_snps_or$ci[pnca_snps_or$mutation == i]
#===============
# Step 4: Iterate through this unique list
# and calculate OR, but only for one snp
# this is test before you apply it all others
#===============
pnca_snps_or$mutation == i
View(pnca_snps_or)
# create an empty dataframe
pnca_snps_or = data.frame(mutation = i)
my_logor -> pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i]
my_or -> pnca_snps_or$OR[pnca_snps_or$mutation == i]
my_pval -> pnca_snps_or$pvalue[pnca_snps_or$mutation == i]
my_zval -> pnca_snps_or$zvalue[pnca_snps_or$mutation == i]
my_se -> pnca_snps_or$logistic_se[pnca_snps_or$mutation == i]
my_ci -> pnca_snps_or$ci[pnca_snps_or$mutation == i]
View(pnca_snps_or_copy)
#===============
# Step 4: Iterate through this unique list
# and calculate OR, but only for one snp
# this is test before you apply it all others
#===============
#reset original df so you don't make a mistake
pnca_snps_or = pnca_snps_or_copy
for (i in pnca_snps_unique){
print(i)
}
pnca_snps_or = pnca_snps_or_copy #2133, 1
#........................................
# create an empty dataframe : uncomment as necessary
pnca_snps_or = data.frame(mutation = c(i, "blank_mut")
#........................................
# create an empty dataframe : uncomment as necessary
pnca_snps_or = data.frame(mutation = c(i, "blank_mut"))
#........................................
# create an empty dataframe : uncomment as necessary
pnca_snps_or = data.frame(mutation = c(i, "blank_mut"))
View(pnca_snps_or)
# IV: corresponds to each unique snp (extracted using grep)
x = as.numeric(grepl(i,raw_data$all_muts_pza))
# DV: pyrazinamide 0 or 1
y = as.numeric(raw_data$pyrazinamide)
table(y,x)
# run glm model
model = glm(y ~ x, family = binomial)
#model = glm(y ~ x, family = binomial(link = "logit"))
summary(model)
#**********
# extract relevant model output
#**********
# extract log OR i.e the Beta estimate of the logistic model for a given snp
my_logor = summary(model)$coefficients[2,1]
print(paste0('Beta:', my_logor))
# extract SE of the logistic model for a given snp
my_se = summary(model)$coefficients[2,2]
print(paste0('SE:', my_se))
# extract Z of the logistic model for a given snp
my_zval = summary(model)$coefficients[2,3]
print(paste0('Z-value:', my_zval))
# Dervive OR i.e exp(my_logor) from the logistic model for a given snp
#my_or = round(exp(summary(model)$coefficients[2,1]), roundto)
my_or = exp(summary(model)$coefficients[2,1])
print(paste0('OR:', my_or))
# sanity check : should be True
log(my_or) == my_logor
# extract P-value of the logistic model for a given snp
my_pval = summary(model)$coefficients[2,4]
print(paste0('P-value:', my_pval))
# extract confint interval of snp (2 steps, since the output is a named number)
ci_mod = exp(confint(model))[2,]
my_ci = paste(ci_mod[["2.5 %"]], ",", ci_mod[["97.5 %"]])
print(paste0('CI:', my_ci))
#*************
# Assign the regression output in the original df
# you can use ('=' or '<-/->')
#*************
#pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i] = my_logor
my_logor -> pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i]
my_or -> pnca_snps_or$OR[pnca_snps_or$mutation == i]
my_pval -> pnca_snps_or$pvalue[pnca_snps_or$mutation == i]
my_zval -> pnca_snps_or$zvalue[pnca_snps_or$mutation == i]
my_se -> pnca_snps_or$logistic_se[pnca_snps_or$mutation == i]
my_ci -> pnca_snps_or$ci[pnca_snps_or$mutation == i]
View(pnca_snps_or)
pnca_snps_or = pnca_snps_or_copy #2133, 1
for (i in pnca_snps_unique){
print(i)
#*************
# start logistic regression model building
#*************
# set the IV and DV for the logistic regression model
# IV: corresponds to each unique snp (extracted using grep)
x = as.numeric(grepl(i,raw_data$all_muts_pza))
# DV: pyrazinamide 0 or 1
y = as.numeric(raw_data$pyrazinamide)
table(y,x)
# run glm model
model = glm(y ~ x, family = binomial)
#model = glm(y ~ x, family = binomial(link = "logit"))
summary(model)
#**********
# extract relevant model output
#**********
# extract log OR i.e the Beta estimate of the logistic model for a given snp
my_logor = summary(model)$coefficients[2,1]
print(paste0('Beta:', my_logor))
# extract SE of the logistic model for a given snp
my_se = summary(model)$coefficients[2,2]
print(paste0('SE:', my_se))
# extract Z of the logistic model for a given snp
my_zval = summary(model)$coefficients[2,3]
print(paste0('Z-value:', my_zval))
# Dervive OR i.e exp(my_logor) from the logistic model for a given snp
#my_or = round(exp(summary(model)$coefficients[2,1]), roundto)
my_or = exp(summary(model)$coefficients[2,1])
print(paste0('OR:', my_or))
# sanity check : should be True
log(my_or) == my_logor
# extract P-value of the logistic model for a given snp
my_pval = summary(model)$coefficients[2,4]
print(paste0('P-value:', my_pval))
# extract confint interval of snp (2 steps, since the output is a named number)
ci_mod = exp(confint(model))[2,]
my_ci = paste(ci_mod[["2.5 %"]], ",", ci_mod[["97.5 %"]])
print(paste0('CI:', my_ci))
#*************
# Assign the regression output in the original df
# you can use ('=' or '<-/->')
#*************
#pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i] = my_logor
my_logor -> pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i]
my_or -> pnca_snps_or$OR[pnca_snps_or$mutation == i]
my_pval -> pnca_snps_or$pvalue[pnca_snps_or$mutation == i]
my_zval -> pnca_snps_or$zvalue[pnca_snps_or$mutation == i]
my_se -> pnca_snps_or$logistic_se[pnca_snps_or$mutation == i]
my_ci -> pnca_snps_or$ci[pnca_snps_or$mutation == i]
}
warnings()
View(pnca_snps_or)
View(pnca_snps_or_copy)
#sanity check
pnca_snps_or$mutation == i1
#sanity check
pnca_snps_or[pnca_snps_or$mutation == i1]
pnca_snps_or[pnca_snps_or$mutation == i2]
pnca_snps_or[pnca_snps_or$mutation == i2,]
pnca_snps_or1 = unique(pnca_snps_or)
write.csv(pnca_snps_or1, "../Data_original/valid_pnca_snps_with_OR.csv")
# you only need it for the unique mutations
pnca_snps_or = unique(pnca_snps_or) #2133, 1
for (i in pnca_snps_unique){
print(i)
#*************
# start logistic regression model building
#*************
# set the IV and DV for the logistic regression model
# IV: corresponds to each unique snp (extracted using grep)
x = as.numeric(grepl(i,raw_data$all_muts_pza))
# DV: pyrazinamide 0 or 1
y = as.numeric(raw_data$pyrazinamide)
table(y,x)
# run glm model
model = glm(y ~ x, family = binomial)
#model = glm(y ~ x, family = binomial(link = "logit"))
summary(model)
#**********
# extract relevant model output
#**********
# extract log OR i.e the Beta estimate of the logistic model for a given snp
my_logor = summary(model)$coefficients[2,1]
print(paste0('Beta:', my_logor))
# extract SE of the logistic model for a given snp
my_se = summary(model)$coefficients[2,2]
print(paste0('SE:', my_se))
# extract Z of the logistic model for a given snp
my_zval = summary(model)$coefficients[2,3]
print(paste0('Z-value:', my_zval))
# Dervive OR i.e exp(my_logor) from the logistic model for a given snp
#my_or = round(exp(summary(model)$coefficients[2,1]), roundto)
my_or = exp(summary(model)$coefficients[2,1])
print(paste0('OR:', my_or))
# sanity check : should be True
log(my_or) == my_logor
# extract P-value of the logistic model for a given snp
my_pval = summary(model)$coefficients[2,4]
print(paste0('P-value:', my_pval))
# extract confint interval of snp (2 steps, since the output is a named number)
ci_mod = exp(confint(model))[2,]
my_ci = paste(ci_mod[["2.5 %"]], ",", ci_mod[["97.5 %"]])
print(paste0('CI:', my_ci))
#*************
# Assign the regression output in the original df
# you can use ('=' or '<-/->')
#*************
#pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i] = my_logor
my_logor -> pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i]
my_or -> pnca_snps_or$OR[pnca_snps_or$mutation == i]
my_pval -> pnca_snps_or$pvalue[pnca_snps_or$mutation == i]
my_zval -> pnca_snps_or$zvalue[pnca_snps_or$mutation == i]
my_se -> pnca_snps_or$logistic_se[pnca_snps_or$mutation == i]
my_ci -> pnca_snps_or$ci[pnca_snps_or$mutation == i]
}
View(pnca_snps_or)
2.290256e+01
1.561132e+06
3.242285e-04
#sanity check
pnca_snps_or[pnca_snps_or$mutation == i1]
pnca_snps_or[pnca_snps_or$mutation == i2,]
write.csv(pnca_snps_or1, "../Data_original/valid_pnca_snps_with_OR.csv")
my_data = read.csv("../Data_original/meta_pza_with_AF.csv"
, stringsAsFactors = FALSE) #11374, 19
View(my_data)
# remove the first column
my_data = my_data[-1] #11374, 18
# check if first col is 'id': should be TRUE
colnames(my_data)[1] == 'id'
# sanity check
snps_all = unique(my_data$mutation)# 337
pnca_snps_or = snps_all
pnca_snps_or = as.data.frame(snps_all)
View(pnca_snps_or)
snps_all[-"true_wt"]
pnca_snps_or = as.data.frame(snps_all[-c(1,1)])
View(pnca_snps_or)
snps_all = as.data.frame(snps_all)
View(snps_all)
#remove true_wt entry
w1 = which(rownames(snps_all) == "true_wt")
View(snps_all)
#remove true_wt entry
w1 = which(snps_all$snps_all == "true_wt")
rm(pnca_snps_or)
pnca_snps_or = snps_all[-w1]
pnca_snps_or = snps_all[,-w1]
pnca_snps_or = as.data.frame(snps_all[-c(1,1)])
#remove true_wt entry
w1 = which(snps_all) == "true_wt"
pnca_snps_or = as.data.frame(snps_all[-c(1,1)])
my_data = read.csv("../Data_original/meta_pza_with_AF.csv"
, stringsAsFactors = FALSE) #11374, 19
# remove the first column
my_data = my_data[-1] #11374, 18
# check if first col is 'id': should be TRUE
colnames(my_data)[1] == 'id'
# sanity check
snps_all = unique(my_data$mutation)# 337
snps_all = as.data.frame(snps_all)
snps_all[-c(1,1)]
pnca_snps_or = as.data.frame(snps_all[-c(1,1)])
pnca_snps_or = as.data.frame(snps_all[, -c(1,1)])
#remove true_wt entry
#w1 = which(snps_all) == "true_wt"
pnca_snps_or = snps_all
pnca_snps_or = pnca_snps_or_copy
#remove true_wt entry
#w1 = which(snps_all) == "true_wt"
pnca_snps_or = snps_all
pnca_snps_or -> pnca_snps_or_copy
#===============
# Step 4: Iterate through this unique list
# and calculate OR for each snp
# and assign to the pnca_snps_or df that has
# each row as a unique snp
#===============
# reset original df so you don't make a mistake: IMPORTANT
pnca_snps_or = pnca_snps_or_copy #2133, 1
# you only need it for the unique mutations
pnca_snps_or = unique(pnca_snps_or) #337, 1
for (i in pnca_snps_unique){
print(i)
#*************
# start logistic regression model building
#*************
# set the IV and DV for the logistic regression model
# IV: corresponds to each unique snp (extracted using grep)
x = as.numeric(grepl(i,raw_data$all_muts_pza))
# DV: pyrazinamide 0 or 1
y = as.numeric(raw_data$pyrazinamide)
table(y,x)
# run glm model
model = glm(y ~ x, family = binomial)
#model = glm(y ~ x, family = binomial(link = "logit"))
summary(model)
#**********
# extract relevant model output
#**********
# extract log OR i.e the Beta estimate of the logistic model for a given snp
my_logor = summary(model)$coefficients[2,1]
print(paste0('Beta:', my_logor))
# extract SE of the logistic model for a given snp
my_se = summary(model)$coefficients[2,2]
print(paste0('SE:', my_se))
# extract Z of the logistic model for a given snp
my_zval = summary(model)$coefficients[2,3]
print(paste0('Z-value:', my_zval))
# Dervive OR i.e exp(my_logor) from the logistic model for a given snp
#my_or = round(exp(summary(model)$coefficients[2,1]), roundto)
my_or = exp(summary(model)$coefficients[2,1])
print(paste0('OR:', my_or))
# sanity check : should be True
log(my_or) == my_logor
# extract P-value of the logistic model for a given snp
my_pval = summary(model)$coefficients[2,4]
print(paste0('P-value:', my_pval))
# extract confint interval of snp (2 steps, since the output is a named number)
ci_mod = exp(confint(model))[2,]
my_ci = paste(ci_mod[["2.5 %"]], ",", ci_mod[["97.5 %"]])
print(paste0('CI:', my_ci))
#*************
# Assign the regression output in the original df
# you can use ('=' or '<-/->')
#*************
#pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i] = my_logor
my_logor -> pnca_snps_or$logistic_logOR[pnca_snps_or$mutation == i]
my_or -> pnca_snps_or$OR[pnca_snps_or$mutation == i]
my_pval -> pnca_snps_or$pvalue[pnca_snps_or$mutation == i]
my_zval -> pnca_snps_or$zvalue[pnca_snps_or$mutation == i]
my_se -> pnca_snps_or$logistic_se[pnca_snps_or$mutation == i]
my_ci -> pnca_snps_or$ci[pnca_snps_or$mutation == i]
}
getwd()
#setwd("~/Documents/git/LSHTM_Y1_PNCA/meta_data_analysis") # work
setwd("~/git/LSHTM_Y1_PNCA/meta_data_analysis") # thinkpad
#setwd("/Users/tanu/git/LSHTM_Y1_PNCA/meta_data_analysis") # mac
getwd()
#===============
# Step 1: read raw data
#===============
raw_data<-read.csv("../Data_original/original_tanushree_data_v2.csv"
,stringsAsFactors = F)[,c("id","pyrazinamide","dr_mutations_pyrazinamide","other_mutations_pyrazinamide")]#19265, 4
raw_data<-raw_data[!is.na(raw_data$pyrazinamide),]#12511, 4
# combine the two mutation columns
raw_data$all_mutations_pyrazinamide<-paste(raw_data$dr_mutations_pyrazinamide, raw_data$other_mutations_pyrazinamide)#12511, 5
head(raw_data$all_mutations_pyrazinamide)
# create yet another column that contains all the mutations but in lower case
raw_data$all_muts_pza = tolower(raw_data$all_mutations_pyrazinamide) #12511, 6
table(grepl("pnca_p",raw_data$all_muts_pza))
#FALSE TRUE
#10603 1908
pnca_snps_or = read.csv("../Data_original/pnca_snps_for_or_calcs.csv"
, stringsAsFactors = F
, header = T) #2133
# subset a snall section to test
#pnca_snps_or_copy = pnca_snps_or
#pnca_snps_or = pnca_snps_or_copy
pnca_snps_unique = unique(pnca_snps_or$mutation) #293
i2 = "pnca_p.trp68gly" # Should exist
grep(i2, pnca_snps_unique)
my_data = read.csv("../Data_original/meta_pza_with_AF.csv"
, stringsAsFactors = FALSE) #11374, 19
# remove the first column
my_data = my_data[-1] #11374, 18
# check if first col is 'id': should be TRUE
colnames(my_data)[1] == 'id'
# sanity check
head(my_data$mutation)
my_data = unique(my_data$mutation)
my_data[!duplicated(my_data$mutation)]
my_data_unique = my_data[!duplicated(my_data$mutation),]
my_data[!duplicated('mutation'),]
my_data_unique = my_data[!duplicated(my_data[,'mutation']),]
my_data_unique = my_data[!duplicated(my_data['mutation']),]
getwd()
setwd("/git/LSHTM_analysis/meta_data_analysis")
getwd()
getwd()
setwd("/git/github/LSHTM_analysis/meta_data_analysis")
getwd()
#===============
# Step 1: read GWAS raw data stored in Data_original/
#===============
infile = read.csv("../Data_original", file.choose(), stringsAsFactors = F))
c = file.choose()
c = file.choose(../Data_original)
c = read.csv(file.choose(), stringsAsFactors = F)
#===============
# Step 1: read GWAS raw data stored in Data_original/
#===============
infile = read.csv(file.choose(), stringsAsFactors = F))
c = read.csv(file.choose(), stringsAsFactors = F)
#===============
# Step 1: read GWAS raw data stored in Data_original/
#===============
infile = read.csv(file.choose(), stringsAsFactors = F)
#===============
# Step 1: read GWAS raw data stored in Data_original/
#===============
infile = read.csv(file.choose(), stringsAsFactors = F)
raw_data = infile[,c("id","pyrazinamide","dr_mutations_pyrazinamide","other_mutations_pyrazinamide")]
outdir = paste0("../mcsm_analysis",drug,"/Data/")
# define output variables
drug = 'pyrazinamide'
outdir = paste0("../mcsm_analysis",drug,"/Data/")
outdir = paste0("../mcsm_analysis/",drug,"/Data/")
outFile = "meta_data_with_AFandOR.csv"
output_filename = paste0(outdir, outFile)
output_filename
pnca_snps_or = read.csv(file.choose()
, stringsAsFactors = F
, header = T)
View(pnca_snps_or)
View(pnca_snps_or)

276
meta_data_analysis/pnca_AF_and_OR_calcs.R
View file

@ -1,16 +1,59 @@
#============================================
# TASK: to calculate allele frequency and OR
# on master data
#===========================================
homedir = '~'
getwd() getwd()
setwd("/git/github/git/LSHTM_analysis/meta_data_analysis") #setwd('~/git/LSHTM_analysis/meta_data_analysis')
setwd(paste0(homedir, '/', 'git/LSHTM_analysis/meta_data_analysis'))
getwd() getwd()
#=============== #%% variable assignment: input and output paths & filenames
# Step 1: read GWAS raw data stored in Data_original/ drug = 'pyrazinamide'
#=============== gene = 'pncA'
infile = read.csv(file.choose(), stringsAsFactors = F) gene_match = paste0(gene,'_p.')
print(gene_match)
raw_data = infile[,c("id" #=======
# input dir
#=======
# file1: Raw data
#indir = 'git/Data/pyrazinamide/input/original'
indir = paste0('git/Data', '/', drug, '/', 'input/original')
in_filename = 'original_tanushree_data_v2.csv'
infile = paste0(homedir, '/', indir, '/', in_filename)
print(paste0('Reading infile:', ' ', infile) )
# file2: file to extract valid snps and add calcs to: pnca_metadata.csv {outfile3 from data extraction script}
indir_metadata = paste0('git/Data', '/', drug, '/', 'output')
in_filename_metadata = 'pnca_metadata.csv'
infile_metadata = paste0(homedir, '/', indir_metadata, '/', in_filename_metadata)
print(paste0('Reading metadata infile:', infile_metadata))
#=========
# output dir
#=========
# output filename in respective section at the time of outputting files
#outdir = 'git/Data/pyrazinamide/output'
outdir = paste0('git/Data', '/', drug, '/', 'output')
out_filename = paste0(tolower(gene),'_', 'meta_data_with_AFandOR.csv')
outfile = paste0(homedir, '/', outdir, '/', out_filename)
print(paste0('Output file with full path:', outfile))
#%% end of variable assignment for input and output files
#===============
# Step 1: Read master/raw data stored in Data/
#===============
raw_data_all = read.csv(infile, stringsAsFactors = F)
raw_data = raw_data_all[,c("id"
, "pyrazinamide" , "pyrazinamide"
, "dr_mutations_pyrazinamide" , "dr_mutations_pyrazinamide"
, "other_mutations_pyrazinamide")] , "other_mutations_pyrazinamide")]
rm(raw_data_all)
rm(indir, in_filename, infile)
##### #####
# 1a: exclude na # 1a: exclude na
@ -18,7 +61,7 @@ raw_data = infile[,c("id"
raw_data = raw_data[!is.na(raw_data$pyrazinamide),] raw_data = raw_data[!is.na(raw_data$pyrazinamide),]
total_samples = length(unique(raw_data$id)) total_samples = length(unique(raw_data$id))
print(total_samples) print(paste0('Total samples without NA in', ' ', drug, 'is:', total_samples))
# sanity check: should be true # sanity check: should be true
is.numeric(total_samples) is.numeric(total_samples)
@ -36,10 +79,15 @@ head(raw_data$all_mutations_pyrazinamide)
raw_data$all_muts_pnca = tolower(raw_data$all_mutations_pyrazinamide) raw_data$all_muts_pnca = tolower(raw_data$all_mutations_pyrazinamide)
# sanity checks # sanity checks
table(grepl("pnca_p",raw_data$all_muts_pnca)) #table(grepl("pnca_p",raw_data$all_muts_pnca))
print(paste0('converting gene match:', gene_match, ' ', 'to lowercase'))
gene_match = tolower(gene_match)
table(grepl(gene_match,raw_data$all_muts_pnca))
# sanity check: should be TRUE # sanity check: should be TRUE
sum(table(grepl("pnca_p",raw_data$all_muts_pnca))) == total_samples #sum(table(grepl("pnca_p",raw_data$all_muts_pnca))) == total_samples
sum(table(grepl(gene_match,raw_data$all_muts_pnca))) == total_samples
# set up variables: can be used for logistic regression as well # set up variables: can be used for logistic regression as well
i = "pnca_p.ala134gly" # has a NA, should NOT exist i = "pnca_p.ala134gly" # has a NA, should NOT exist
@ -56,17 +104,40 @@ table(mut, dst)
#fisher.test(table(mut, dst)) #fisher.test(table(mut, dst))
#table(mut) #table(mut)
###### read list of muts to calculate OR for (fname3 from pnca_data_extraction.py) #===============
pnca_snps_or = read.csv(file.choose() # Step 2: Read valid snps for which OR can be calculated (infile_comp_snps.csv)
#===============
print(paste0('Reading metadata infile:', infile_metadata))
pnca_metadata = read.csv(infile_metadata
# , file.choose()
, stringsAsFactors = F , stringsAsFactors = F
, header = T) , header = T)
# extract unique snps to iterate over for AF and OR calcs
# total no of unique snps
# AF and OR calculations
# clear variables
rm(homedir, in_filename, indir, infile)
rm(indir_metadata, infile_metadata, in_filename_metadata)
# count na in pyrazinamide column
tot_pza_na = sum(is.na(pnca_metadata$pyrazinamide))
expected_rows = nrow(pnca_metadata) - tot_pza_na
# drop na from the pyrazinamide colum
pnca_snps_or = pnca_metadata[!is.na(pnca_metadata$pyrazinamide),]
# sanity check
if(nrow(pnca_snps_or) == expected_rows){
print('PASS: no. of rows match with expected_rows')
} else{
print('FAIL: nrows mismatch.')
}
# extract unique snps to iterate over for AF and OR calcs
pnca_snps_unique = unique(pnca_snps_or$mutation) pnca_snps_unique = unique(pnca_snps_or$mutation)
print(paste0('Total no. of distinct comp snps to perform OR calcs: ', length(pnca_snps_unique)))
# Define OR function # Define OR function
x = as.numeric(mut) x = as.numeric(mut)
y = dst y = dst
@ -111,131 +182,106 @@ afs['pnca_p.trp68gly']
afs['pnca_p.gln10pro'] afs['pnca_p.gln10pro']
afs['pnca_p.leu4ser'] afs['pnca_p.leu4ser']
#plot(density(log(ors))) plot(density(log(ors)))
#plot(-log10(pvals)) plot(-log10(pvals))
#hist(log(ors) hist(log(ors)
# ,breaks = 100 , breaks = 100
# ) )
# subset df cols to add to the calc param df # FIXME: could be good to add a sanity check
pnca_snps_cols = pnca_snps_or[c('mutation_info', 'mutation', 'Mutationinformation')] if (table(names(ors) == names(pvals)) & table(names(ors) == names(afs)) & table(names(pvals) == names(afs)) == length(pnca_snps_unique)){
pnca_snps_cols = pnca_snps_cols[!duplicated(pnca_snps_cols$mutation),] print('PASS: names of ors, pvals and afs match: proceed with combining into a single df')
} else{
rownames(pnca_snps_cols) = pnca_snps_cols$mutation print('FAIL: names of ors, pvals and afs mismatch')
head(rownames(pnca_snps_cols)) }
#snps_with_AF_and_OR
# combine # combine
comb_AF_and_OR = data.frame(ors, pvals, afs) comb_AF_and_OR = data.frame(ors, pvals, afs)
head(rownames(comb_AF_and_OR)) head(rownames(comb_AF_and_OR))
# sanity checks: should be the same # add rownames of comb_AF_and_OR as an extra column 'mutation' to allow merging based on this column
dim(comb_AF_and_OR); dim(pnca_snps_cols) comb_AF_and_OR$mutation = rownames(comb_AF_and_OR)
table(rownames(comb_AF_and_OR)%in%rownames(pnca_snps_cols))
table(rownames(pnca_snps_cols)%in%rownames(comb_AF_and_OR))
# merge the above two df whose dim you checked
snps_with_AF_and_OR = merge(comb_AF_and_OR, pnca_snps_cols
, by = "row.names"
# , all.x = T
)
#rm(pnca_snps_cols, pnca_snps_or, raw_data)
#===============
# Step 3: Read data file where you will add the calculated OR
# Note: this is the big file with one-many relationship between snps and lineages
# i.e fname4 from 'pnca_extraction.py'
#===============
my_data = read.csv(file.choose()
, row.names = 1
, stringsAsFactors = FALSE)
head(my_data)
length(unique(my_data$id))
# check if first col is 'id': should be TRUE
colnames(my_data)[1] == 'id'
# sanity check # sanity check
head(my_data$mutation) if (table(rownames(comb_AF_and_OR) == comb_AF_and_OR$mutation)){
print('PASS: rownames and mutaion col values match')
}else{
print('FAIL: rownames and mutation col values mismatch')
}
# FILES TO MERGE: ############
# comb_AF_and_OR: file containing OR # Merge 1:
# my_data = big meta data file ###########
# linking column: mutation df1 = pnca_metadata
df2 = comb_AF_and_OR
head(my_data) head(df1$mutation); head(df2$mutation)
merged_df = merge(my_data # big file
, snps_with_AF_and_OR # small (afor file) # FIXME: newlines
print(paste0('merging two dfs: '
,'\ndf1 (big df i.e. meta data) nrows: ', nrow(df1)
,'\ndf2 (small df i.e af, or, pval) nrows: ', nrow(df2)
, 'expected rows in merged df: ', nrow(df1), 'expected cols in merged_df: ', (ncol(df1) + ncol(df2) - 1)))
merged_df = merge(df1 # big file
, df2 # small (afor file)
, by = "mutation" , by = "mutation"
, all.x = T) # because you want all the entries of the meta data , all.x = T) # because you want all the entries of the meta data
# sanity checks: should be True # sanity check
# FIXME: I have checked this manually, but make it so it is a pass or a fail! if(ncol(merged_df) == (ncol(df1) + ncol(df2) - 1)){
comb_AF_and_OR[rownames(comb_AF_and_OR) == "pnca_p.gln10pro",]$ors print(paste0('PASS: no. of cols is as expected: ', ncol(merged_df)))
merged_df[merged_df$Mutationinformation.x == "Q10P",]$ors } else{
print('FAIL: no.of cols mistmatch')
}
merged_df[merged_df$Mutationinformation.x == "Q10P",] # quick check
i = "pnca_p.ala134gly" # has all NAs in pyrazinamide, should be NA in ors, etc.
# sanity check: very important! merged_df[merged_df$mutation == i,]
colnames(merged_df)
table(merged_df$mutation_info.x == merged_df$mutation_info.y)
#FIXME: what happened to other 7 and FALSE
table(merged_df$Mutationinformation.x == merged_df$Mutationinformation.y)
# problem
identical(merged_df$Mutationinformation.x, merged_df$Mutationinformation.y)
#merged_df[merged_df$Mutationinformation.x != merged_df$Mutationinformation.y,]
#throw away the y because that is a smaller df
d1 = which(colnames(merged_df) == "mutation_info.y") #21
d2 = which(colnames(merged_df) == "Mutationinformation.y") #22
merged_df2 = merged_df[-c(d1, d2)] #3093 20
colnames(merged_df2)
# rename cols
colnames(merged_df2)[colnames(merged_df2)== "mutation_info.x"] <- "mutation_info"
colnames(merged_df2)[colnames(merged_df2)== "Mutationinformation.x"] <- "Mutationinformation"
colnames(merged_df2)
# should be 0
sum(is.na(merged_df2$Mutationinformation))
# count na in each column # count na in each column
na_count = sapply(merged_df2, function(y) sum(length(which(is.na(y))))); na_count na_count = sapply(merged_df, function(y) sum(length(which(is.na(y))))); na_count
# only some or and Af should be NA # only some or and Af should be NA
#Row.names ors pvals afs #Row.names ors pvals afs
#81 81 81 81 #63 63 63 63
# reassign custom colnames
colnames(merged_df)[colnames(merged_df)== "ors"] <- "OR"
colnames(merged_df)[colnames(merged_df)== "afs"] <- "AF"
colnames(merged_df)[colnames(merged_df)== "pvals"] <- "pvalue"
colnames(merged_df2)[colnames(merged_df2)== "ors"] <- "OR" colnames(merged_df)
colnames(merged_df2)[colnames(merged_df2)== "afs"] <- "AF"
colnames(merged_df2)[colnames(merged_df2)== "pvals"] <- "pvalue"
colnames(merged_df2)
# add log OR and neglog pvalue # add log OR and neglog pvalue
merged_df2$logor = log(merged_df2$OR) merged_df$logor = log(merged_df$OR)
is.numeric(merged_df2$logor) is.numeric(merged_df$logor)
merged_df2$neglog10pvalue = -log10(merged_df2$pvalue) merged_df$neglog10pvalue = -log10(merged_df$pvalue)
is.numeric(merged_df2$neglog10pvalue) is.numeric(merged_df$neglog10pvalue)
# write file out merged_df$AF_percent = merged_df$AF*100
#write.csv(merged_df, "../Data/meta_data_with_AFandOR_JP_TT.csv") is.numeric(merged_df$AF_percent)
# define output variables # check AFs
drug = 'pyrazinamide' #i = 'pnca_p.trp68gly'
out_dir = paste0("../mcsm_analysis/",drug,"/Data/") i = 'pnca_p.gln10pro'
outFile = "meta_data_with_AFandOR.csv" #i = 'pnca_p.leu4ser'
output_filename = paste0(outdir, outFile) merged_df[merged_df$mutation == i,]
write.csv(merged_df2, output_filename # FIXME: harcoding (beware!), NOT FATAL though!
ncol_added = 3
print(paste0('Added', ncol_added, ' ', 'more cols to merged_df i.e log10 OR and -log10 P-val: '
, 'no. of cols in merged_df now: ', ncol(merged_df)))
#%% write file out: pnca_meta_data_with_AFandOR
print(paste0('writing output file in: '
, 'Filename: ', out_filename
, 'Path:', outdir))
write.csv(merged_df, outfile
, row.names = F) , row.names = F)
print(paste0('Finished writing:', out_filename, '\nExpected no. of cols:', ncol(merged_df)))
print('======================================================================')
rm(out_filename)

106
meta_data_analysis/pnca_data_extraction.py
View file

@ -36,9 +36,10 @@ import numpy as np
# 1) pnca_ambiguous_muts.csv # 1) pnca_ambiguous_muts.csv
# 2) pnca_mcsm_snps.csv # 2) pnca_mcsm_snps.csv
# 3) pnca_metadata.csv # 3) pnca_metadata.csv
# 4) pnca_comp_snps.csv # 4) pnca_comp_snps.csv <---deleted>
# 5) pnca_all_muts_msa.csv
# 6) pnca_mutational_positons.csv # 4) pnca_all_muts_msa.csv
# 5) pnca_mutational_positons.csv
#======================================================== #========================================================
#%% specify homedir as python doesn't recognise tilde #%% specify homedir as python doesn't recognise tilde
homedir = os.path.expanduser('~') homedir = os.path.expanduser('~')
@ -52,23 +53,25 @@ os.getcwd()
from reference_dict import my_aa_dict #CHECK DIR STRUC THERE! from reference_dict import my_aa_dict #CHECK DIR STRUC THERE!
#======================================================== #========================================================
#drug = 'pyrazinamide' #%% variable assignment: input and output paths & filenames
drug = 'pyrazinamide'
gene = 'pncA' gene = 'pncA'
gene_match = gene + '_p.' gene_match = gene + '_p.'
#%% specify variables for input and output paths and filenames
#======= #=======
# input dir # input dir
#======= #=======
indir = 'git/Data/pyrazinamide/input/original' #indir = 'git/Data/pyrazinamide/input/original'
indir = 'git/Data' + '/' + drug + '/' + 'input/original'
#========= #=========
# output dir # output dir
#========= #=========
# several output files # several output files
# output filenames in respective sections at the time of outputting files # output filenames in respective sections at the time of outputting files
outdir = 'git/Data/pyrazinamide/output' #outdir = 'git/Data/pyrazinamide/output'
outdir = 'git/Data' + '/' + drug + '/' + 'output'
#%%end of variable assignment for input and output files #%%end of variable assignment for input and output files
#============================================================================== #==============================================================================
#%% Read files #%% Read files
@ -334,6 +337,8 @@ print('Writing file: common ids:\n',
common_ids.to_csv(outfile0) common_ids.to_csv(outfile0)
print('======================================================================') print('======================================================================')
del(out_filename0)
# clear variables # clear variables
del(dr_id, other_id, meta_data_dr, meta_data_other, common_ids, common_mut_ids, common_ids2) del(dr_id, other_id, meta_data_dr, meta_data_other, common_ids, common_mut_ids, common_ids2)
@ -701,21 +706,6 @@ del(c1, c2, col_to_split1, col_to_split2, comp_pnca_samples, dr_WF0, dr_df, dr_m
#%% end of data extraction and some files writing. Below are some more files writing. #%% end of data extraction and some files writing. Below are some more files writing.
#%%: write file: ambiguous muts #%%: write file: ambiguous muts
# uncomment as necessary # uncomment as necessary
#print(outdir) #print(outdir)
@ -735,6 +725,8 @@ inspect.to_csv(outfile1)
print('Finished writing:', out_filename1, '\nExpected no. of rows (no. of samples with the ambiguous muts present):', dr_muts.isin(other_muts).sum() + other_muts.isin(dr_muts).sum()) print('Finished writing:', out_filename1, '\nExpected no. of rows (no. of samples with the ambiguous muts present):', dr_muts.isin(other_muts).sum() + other_muts.isin(dr_muts).sum())
print('======================================================================') print('======================================================================')
del(out_filename1) del(out_filename1)
#%% #%%
#=========== #===========
# Split 'mutation' column into three: wild_type, position and # Split 'mutation' column into three: wild_type, position and
@ -891,6 +883,8 @@ print('Finished writing:', out_filename2,
'\nNo. of rows:', len(snps_only) ) '\nNo. of rows:', len(snps_only) )
print('======================================================================') print('======================================================================')
del(out_filename2) del(out_filename2)
#%% Write file: pnca_metadata (i.e pnca_LF1) #%% Write file: pnca_metadata (i.e pnca_LF1)
# where each row has UNIQUE mutations NOT unique sample ids # where each row has UNIQUE mutations NOT unique sample ids
out_filename3 = gene.lower() + '_' + 'metadata.csv' out_filename3 = gene.lower() + '_' + 'metadata.csv'
@ -903,45 +897,10 @@ pnca_LF1.to_csv(outfile3, header = True, index = False)
print('Finished writing:', out_filename3, print('Finished writing:', out_filename3,
'\nNo. of rows:', len(pnca_LF1), '\nNo. of rows:', len(pnca_LF1),
'\nNo. of cols:', len(pnca_LF1.columns) ) '\nNo. of cols:', len(pnca_LF1.columns) )
print('======================================================================') print('======================================================================')
del(out_filename3)
#%% Write file: comp SNPs (i.e snps without any corresponding 'NA' in the <drug>
# column to allow OR calcs)
# remove NA from pyrazinamide cols
pnca_LF2 = pnca_LF1.dropna(subset=['pyrazinamide'])
print('extracting OR muts by removing NAs from pyrazinamide cols')
if pnca_LF2.pyrazinamide.isna().sum() > 0:
print('FAIL: NAs NOT removed successfully')
else:
print('PASS: NAs removed successfully')
# extracting comp snps only
comp_snps_only = pd.DataFrame(pnca_LF2['mutation'].unique())
#print('Total no. of comp snps:', len(comp_snps_only))
comp_snps_only.head()
# assign column name
comp_snps_only.columns = ['mutation']
# count how many positions this corresponds to
comp_pos_only = pd.DataFrame(pnca_LF2['position'].unique())
#print('Total no. of pos corresponding to comp_snps:', len(comp_pos_only))
out_filename4 = gene.lower() + '_' + 'comp_snps.csv'
outfile4 = homedir + '/' + outdir + '/' + out_filename4
print('Writing file: comp snps to allow OR calcs',
'\nFilename:', out_filename4,
'\nPath:', homedir + '/' + outdir,
'\nNo. of comp muts:', len(comp_snps_only),
'\nNo. of distinct positions for comp muts:', len(comp_pos_only) )
comp_snps_only.to_csv(outfile4, header = True, index = False)
print('Finished writing:', out_filename4,
'\nNo. of rows:', len(comp_snps_only) )
#%% write file: mCSM style but with repitions for MSA and logo plots #%% write file: mCSM style but with repitions for MSA and logo plots
all_muts_msa = pd.DataFrame(pnca_LF1['Mutationinformation']) all_muts_msa = pd.DataFrame(pnca_LF1['Mutationinformation'])
all_muts_msa.head() all_muts_msa.head()
@ -970,21 +929,22 @@ else:
'\nDebug please!') '\nDebug please!')
print('======================================================================') print('======================================================================')
out_filename5 = gene.lower() + '_' + 'all_muts_msa.csv' out_filename4 = gene.lower() + '_' + 'all_muts_msa.csv'
outfile5 = homedir + '/' + outdir + '/' + out_filename5 outfile4 = homedir + '/' + outdir + '/' + out_filename4
print('Writing file: mCSM style muts for msa', print('Writing file: mCSM style muts for msa',
'\nmutation format (SNP): {Wt}<POS>{Mut}', '\nmutation format (SNP): {Wt}<POS>{Mut}',
'\nNo.of lines of msa:', len(all_muts_msa), '\nNo.of lines of msa:', len(all_muts_msa),
'\nFilename:', out_filename5, '\nFilename:', out_filename4,
'\nPath:', homedir +'/'+ outdir) '\nPath:', homedir +'/'+ outdir)
all_muts_msa_sorted.to_csv(outfile5, header = False, index = False) all_muts_msa_sorted.to_csv(outfile4, header = False, index = False)
print('Finished writing:', out_filename5, print('Finished writing:', out_filename4,
'\nNo. of rows:', len(all_muts_msa) ) '\nNo. of rows:', len(all_muts_msa) )
print('======================================================================') print('======================================================================')
del(out_filename5) del(out_filename4)
#%% write file for mutational positions #%% write file for mutational positions
# count how many positions this corresponds to # count how many positions this corresponds to
@ -999,20 +959,22 @@ pos_only.position.dtype
# sort by position value # sort by position value
pos_only_sorted = pos_only.sort_values(by = 'position', ascending = True) pos_only_sorted = pos_only.sort_values(by = 'position', ascending = True)
out_filename6 = gene.lower() + '_' + 'mutational_positons.csv' out_filename5 = gene.lower() + '_' + 'mutational_positons.csv'
outfile6 = homedir + '/' + outdir + '/' + out_filename6 outfile5 = homedir + '/' + outdir + '/' + out_filename5
print('Writing file: mutational positions', print('Writing file: mutational positions',
'\nNo. of distinct positions:', len(pos_only_sorted), '\nNo. of distinct positions:', len(pos_only_sorted),
'\nFilename:', out_filename6, '\nFilename:', out_filename5,
'\nPath:', homedir +'/'+ outdir) '\nPath:', homedir +'/'+ outdir)
pos_only_sorted.to_csv(outfile6, header = True, index = False) pos_only_sorted.to_csv(outfile5, header = True, index = False)
print('Finished writing:', out_filename6, print('Finished writing:', out_filename5,
'\nNo. of rows:', len(pos_only_sorted) ) '\nNo. of rows:', len(pos_only_sorted) )
print('======================================================================') print('======================================================================')
del(out_filename6) del(out_filename5)
#%% end of script #%% end of script
print('======================================================================') print('======================================================================')
print(u'\u2698' * 50, print(u'\u2698' * 50,