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script for calcuating various OR & output csv

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This commit is contained in:
Tanushree Tunstall 2020-06-23 13:07:29 +01:00
parent a1cc7ee33d
commit 003b22ce3f
2 changed files with 117 additions and 305 deletions
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10
scripts/af_or_calcs_scratch.R
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@ -167,7 +167,7 @@ cat(paste0('Total no. of distinct comp snps to perform OR calcs: ', length(gene_
#x = as.numeric(mut)
#y = dst
custom_chisq_or = function(x,y){
mychisq_or = function(x,y){
tab = as.matrix(table(x,y))
a = tab[2,2]
if (a==0){ a<-0.5}
@ -232,7 +232,7 @@ pval_fisher = fisher.test(table(mut, dst))$p.value; print(paste0('pval fisher:',
#3) custom chisq
or_mychisq = custom_chisq_or(mut,dst)
or_mychisq = mychisq_or(mut,dst)
#4) logistic
summary(model<-glm(dst ~ mut, family = binomial))
@ -277,7 +277,7 @@ snps
# custom chisq
ors = sapply(snps,function(m){
mut = grepl(m,raw_data$all_muts_gene)
custom_chisq_or(mut,dst)
mychisq_or(mut,dst)
})
head(ors)
@ -423,7 +423,7 @@ x = sapply(snps,function(m){
ci_upper_logistic = ci_mod[["97.5 %"]]
# custom_chisq and fisher: OR p-value and CI
or_mychisq = custom_chisq_or(dst, mut)
or_mychisq = mychisq_or(dst, mut)
or_fisher = fisher.test(dst, mut)$estimate
or_fisher = or_fisher[[1]]
@ -523,7 +523,7 @@ for (i in snps){
#=====================
# custom chi square
#=====================
or_mychisq = custom_chisq_or(mut,dst)
or_mychisq = mychisq_or(mut,dst)
#=====================
# chi square