tianshilu / netie Goto Github PK

hi,
i want to run netie, and i have run the pyclone and got the results, but i don't understand what the neo_load is, i checked the QBRC-neoantigen pipeline and still can't find the neo_load. Can you please tell me how to calculate neo_load?

Thanks !

Hi,

I got a result of NA after I run netie with example data, and here are my codes:

example_input1= read.table('netie-main/example/example_input1.txt', header=T,sep='\t',stringsAsFactors = F)

netie(example_input1,
      sigma_square = 100000 ,
      alpha = 10,
      beta = 2,
      sigma_p_sqr = 0.1,
      sigma_a_sqr = NULL,
      max_iter =100000,
      cellular_clock='variant_allele_frequency',
      cellular_prevalence_min=0.02,
      keep_mutations_number=2,
      keep_neoantigen_encoding_mutations_number=1,
      multi_sample = F)

Is there something wrong with my codes? Looking forward to your reply!

Hi tianshi,

I believe Netie is a quite innovative tool. I wonder which is a more suitable way to calculate the neo_load for each mutation,
should I allow annotations for each mutation against multiple transcripts or select a single representative transcript?
There are some mutations with neo_load > 1 in your example input, does it means that you kept all transcripts into consideration?

Look forward to your favourable reply! Appreciate!