af and or calcs, not merging

scripts/AF_and_OR_calcs.R

@@ -9,7 +9,7 @@ setwd('~/git/LSHTM_analysis/scripts')
 getwd()
   
 options(scipen = 999) #disabling scientific notation in R.
-options(scipen = 4)  
+#options(scipen = 4)  
 
 #%% variable assignment: input and output paths & filenames
 drug = 'pyrazinamide'
@@ -40,7 +40,8 @@ cat(paste0('Reading infile2: gene associated metadata:', infile_metadata))
 #===========
 # outdir = 'git/Data/pyrazinamide/output'
 outdir = paste0('~/git/Data', '/', drug, '/', 'output')
-out_filename = paste0(tolower(gene),'_', 'meta_data_with_AF_OR.csv')
+#out_filename = paste0(tolower(gene), '_meta_data_with_AF_OR.csv')
+out_filename = paste0(tolower(gene), '_AF_OR.csv')
 outfile = paste0(outdir, '/', out_filename)
 cat(paste0('Output file with full path:', outfile))
 #%% end of variable assignment for input and output files
@@ -261,7 +262,7 @@ statistic_chi = sapply(gene_snps_unique,function(m){
 })
 
 # statistic_chi: has suffix added of '.X-squared'
-head(statistic_chi)  
+stat_chi = statistic_chi
 
 # remove suffix
 names(stat_chi) = gsub(".X-squared", "", names(statistic_chi))
@@ -389,7 +390,6 @@ hist(log(ors)
      , breaks = 100)
 
 # sanity check: if names are equal (just for 3 vars)
-
 all(sapply(list(names(afs)
                 , names(pvals_chi)
                 , names(statistic_chi) # should return False
@@ -445,11 +445,7 @@ comb_AF_and_OR = data.frame(afs
                             , ci_ub_fisher
                             , pvals_logistic
                             , ors_logistic)
-                           
+                       
-
-
-
-
 cat('No. of rows in comb_AF_and_OR: ', nrow(comb_AF_and_OR)
     , '\nNo. of cols in comb_AF_and_OR: ', ncol(comb_AF_and_OR))
 
@@ -464,11 +460,28 @@ if (table(rownames(comb_AF_and_OR) == comb_AF_and_OR$mutation)){
 }else{
   cat('FAIL: rownames and mutation col values mismatch')
 }
+#########################################################
+# write file out: pnca_AF_OR
+#########################################################
+cat(paste0('writing output file: '
+           , '\nFilename: ', outfile))
+
+write.csv(comb_AF_and_OR, outfile
+          , row.names = F)
+
+cat(paste0('Finished writing:'
+           , out_filename
+           , '\nNo. of rows: ', nrow(comb_AF_and_OR)
+           , '\nNo. of cols: ', ncol(comb_AF_and_OR)))
+#************************************************
+cat('======================================================================')
+rm(out_filename)
+cat('End of script: calculated AF, OR, pvalues and saved file')
 
 #########################################################
 # 3: Merge meta data file + calculated num params
 #########################################################
-df1 = pnca_metadata
+df1 = gene_metadata
 df2 = comb_AF_and_OR
 
 cat('checking commom col of the two dfs before merging:'
@@ -509,10 +522,10 @@ if ( identical(na_count[[length(na_count)]], na_count[[length(na_count)-1]], na_
 }
 
 # reassign custom colnames
-cat('Assigning custom colnames for the calculated params...')
+#cat('Assigning custom colnames for the calculated params...')
-colnames(merged_df)[colnames(merged_df)== "ors"] <- "OR"
+#colnames(merged_df)[colnames(merged_df)== "ors"] <- "OR"
-colnames(merged_df)[colnames(merged_df)== "pvals"] <- "pvalue"
+#colnames(merged_df)[colnames(merged_df)== "pvals"] <- "pvalue"
-colnames(merged_df)[colnames(merged_df)== "afs"] <- "AF"
+#colnames(merged_df)[colnames(merged_df)== "afs"] <- "AF"
 
 colnames(merged_df)