Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models

This is the data repository to the manuscript "Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models". It contains a minimal data set to reproduce all results that don't compromise the privacy concerns. The repository contains the following data: adaptscore_acute.csv A csv file that contains the estimated adaptation scores for the acute data set with HLA I model. adaptscore_leftout.csv A csv file that contains the estimated adaptation scores for the leftout data set with the joint HLA I and HLA II model adaptscore_training.csv A csv file that contains the estimated adaptation scores for the traininig data set with the joint HLA I and HLA II model adaptscore_training_hla1_without_clin.csv A csv file that contains the estimated adaptation scores for the training data set with the HLA I model (via cross-validation) adaptscore_training_seed2.csv A csv file that contains the estimated adaptation scores for the training data set with the joint HLA I and HLA II model via cross-validation with another seed env_leftout.fasta A fasta file that contains the consensus nucleotide sequences for the env protein for the leftout data set env_nt_274.fasta A fasta file that contains the consensus nucleotide sequences for the env protein for the training data set gag_leftout.fasta A fasta file that contains the consensus nucleotide sequences for the gag protein for the leftout data set gag_nt_274.fasta A fasta file that contains the consensus nucleotide sequences for the gag protein for the training data se