doAssociationAnalysis: Check for taxa-metadata associations

In RIVM-IIV-Microbiome/biomeStats: Methods for carrying out association studies of the microbiome

Check for taxa-metadata associations

Description

Check for taxa-metadata associations

Usage

doAssociationAnalysis(
  data_for_testing,
  B = 1e+05,
  no_of_factors = NULL,
  aux_columns = NULL,
  log_scale = TRUE,
  nominal_bound_on_FDR = 0.25,
  phen_data = NULL,
  compare_label = "case_control",
  aux_TYPES = NULL,
  cat_ypes = NULL,
  path_loc = ".",
  name_of_stratification = "Sex and age-group",
  verbose = TRUE
)

Arguments

data_for_testing	A data frame combined from prepTaxaAbundanceData and prepSampleData
B	Resampling default to 100000
no_of_factors	Number of factor from 'data_for_testing' to test.
aux_columns	specific column numbers with taxa abundances.
log_scale	Logical. Plot scale. Default and suggested TRUE
nominal_bound_on_FDR	cut-off for multiple testing. Default=0.25
phen_data	data frame output from prepSampleData()
compare_label	label to save files.
aux_TYPES	How to treat each of the variables in the data_for_testing
cat_ypes	Categorical to plot proportions positive
path_loc	Location to store/save output
name_of_stratification	label of stratum e.g."Sex and age-group"
verbose	TRUE

Details

The associations between taxa and metadata variables are tested. These are done using the method/approach described by JA Ferreira and S Fuentes https://doi.org/10.1093/bib/bbz077

Author(s)

Sudarshan A. Shetty

References

Ferreira JA, Fuentes S. (2020). Some comments on certain statistical aspects of the study of the microbiome. Briefings in bioinformatics 21(4), pp.1487-1494. https://doi.org/10.1093/bib/bbz077

RIVM-IIV-Microbiome/biomeStats documentation built on Sept. 14, 2022, 5:15 p.m.