Confidence score and p-value

TRON-Bioinformatics / seq2HLA

In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.

MIT License

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Confidence score and p-value #10

Open yuanfeng719 opened 1 year ago

yuanfeng719 commented 1 year ago

Hi,

I am currently analyzing the seq2HLA outputs, and I have a question about the definition of the confidence scores. Are they equal to Pvalues or 1 - Pvalues? Is this value the higher the better?

I really appreciate your help!!

Yuan

farzadhallaji commented 1 year ago

the confidence is 1 minus the 2nd largest p-value, and the credibility is the largest p-value I guess