compute_bio_phewas: compute_bio_phewas computes the PheWAS analysis on numeric...
In aneuraz/multimodalPhewas: multiWAS

compute_bio_phewas computes the PheWAS analysis on numeric biological test results

compute_bio_phewas(bio, patients, direction = "SUP", bio_min_occur = 1,
  zero_controls_add = 2, patients_min_concept = NULL, with_boot = FALSE,
  perm = 1000, boot_all = FALSE, fdr_threshold = 0.05,
  analysis_type = "poisson", progress = NULL, cores = 1)

`bio`	bio data.frame from the 'get_data_from_num' function
`patients`	patients data.frame from the 'get_data_from_num' function
`direction`	one of c('SUP', 'INF') to perform the analysis on results above the normal range (SUP) or below the normal range(INF)
`bio_min_occur`	integer. minimum number of occurrences of the biological test result in the dataset to be analyzed
`zero_controls_add`	integer. number of simulated patients to add to the control group for a given if there is no occurrence of this concept in the control group. This trick allows to compute a pvalue in this situation.
`patients_min_concept`	integer. minimum number of unique concept for a patient to be included in the analysis
`with_boot`	logical. perform a bootstrap on the results
`perm`	integer. number of permutations for the bootstrap
`boot_all`	logical. perform a bootstrap on all the results or only on the results with FDR corrected p.value < fdr_threshold
`fdr_threshold`	maximum FDR corrected p.value to perform the bootstrap
`analysis_type`	one of c('poisson', 'binomial') for the type of analysis to perform
`progress`	progress bar object