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Tanushree Tunstall 2022-07-08 13:53:17 +01:00
parent 5577f5b195
commit 23799275a0
3 changed files with 49 additions and 31 deletions
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22
scripts/count_vars_ML.R
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@ -4,7 +4,7 @@
#source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/pnca.R")
source("~/git/LSHTM_analysis/config/pnca.R")
source("~/git/LSHTM_analysis/config/rpob.R")
#############################
@ -55,7 +55,7 @@ if (check12) {
cat('\nPASS: dst mode labels verified. merged_df3 CAN be trusted! ')
}else{
stop('FAIL: Something is wrong with the dst_mode column. Quitting!')
``}
}
#==========================
# CHECK: active site labels
@ -189,6 +189,24 @@ if ( all( check12 && aa_check1 && aa_check2 && a1 && b1 && a2 && b2 && l1 && l2
#quit()
}
#%%###################################################################
# check merged_df3
check_mdf3 = merged_df3[, cols_sel]
check_mdf3T = table(check_mdf3$mutationinformation, check_mdf3$dst_mode)
ft_mdf3 = as.data.frame.matrix(check_mdf3T)
#==================
# CHECK: dst mode
#===================
dst_check_mdf3 = all((ft_mdf3[,1]==0)==(ft_mdf3[,2]!=0)); dst_check_mdf3
sel = c("mutationinformation", "dst", "dst_mode")
a = merged_df3[, sel]
str(a)
# write file
# outfile_merged_df3 = paste0(outdir, '/', tolower(gene), '_merged_df3.csv')
# outfile_merged_df3