compute_phewas: compute_phewas

In aneuraz/multiWAS: multiWAS

Description

computes the PheWAS analysis on concepts (UMLS concepts extracted from free text)

Usage

compute_phewas(concepts, patients, concepts_min_occur = 5,
  zero_controls_add = 2, min_concept = NULL, with_boot = FALSE,
  perm = 1000, boot_all = FALSE, fdr_threshold = 0.05, progress = NULL,
  cores = 1)

Arguments

concepts	concepts data.frame from the 'get_data_from_num' function
patients	patients data.frame from the 'get_data_from_num' function
concepts_min_occur	integer. minimum number of occurrences of the concept 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.
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
progress	progress bar object

aneuraz/multiWAS documentation built on May 14, 2019, 2:37 p.m.