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Tanushree Tunstall 2022-07-12 10:12:41 +01:00
parent 33e3b5a0a6
commit a590354f15
2 changed files with 10 additions and 6 deletions
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10
scripts/count_vars_ML.R
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@ -228,10 +228,12 @@ length(unique((df3$mutationinformation)))
# #
# #dm _om # #dm _om
table(df3$mutation_info) table(df3$mutation_info)
table(df3$mutation_info_labels)
table(df3$mutation_info_orig) table(df3$mutation_info_orig)
table(df3$mutation_info_labels_orig) table(df3$mutation_info_labels_orig)
table(df3$mutation_info_labels) # different, and matches dst_mode
table(df3$dst_mode)
# test_set # test_set
na_count <-sapply(df3, function(y) sum(length(which(is.na(y))))) na_count <-sapply(df3, function(y) sum(length(which(is.na(y)))))
na_count[drug] na_count[drug]
@ -246,8 +248,10 @@ table(df3[drug])
df3_complete = df3 df3_complete = df3
table(df3_complete$dst_mode) table(df3_complete$dst_mode)
comp_lin_all = df3_complete[df3_complete$lineage_labels%in%c("L1", "L2", "L3", "L4"),]
table(comp_lin_all$lineage); sum(table(comp_lin_all$lineage))
df3_actual = df3[!is.na(df3$dst), ] df3_actual = df3[!is.na(df3$dst), ]
table(df3_actual$dst_mode) table(df3_actual$dst_mode)
comp_lin_actual = df3_actual[df3_actual$lineage_labels%in%c("L1", "L2", "L3", "L4"),]
table(comp_lin_actual$lineage); sum(table(comp_lin_actual$lineage))

6
scripts/ml/ml_iterator.py
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@ -41,9 +41,9 @@ gene_model_paramD = {'data_combined_model' : False
############################################################################### ###############################################################################
#ml_genes = ["pncA", "embB", "katG", "rpoB", "gid"] #ml_genes = ["pncA", "embB", "katG", "rpoB", "gid"]
ml_gene_drugD = {'pncA' : 'pyrazinamide' ml_gene_drugD = {#'pncA' : 'pyrazinamide'
, 'embB' : 'ethambutol' # 'embB' : 'ethambutol'
, 'katG' : 'isoniazid' 'katG' : 'isoniazid'
, 'rpoB' : 'rifampicin' , 'rpoB' : 'rifampicin'
, 'gid' : 'streptomycin' , 'gid' : 'streptomycin'
} }