MWAS_bootstrapping: MWAS bootstrap resampling

In MWASTools: MWASTools: an integrated pipeline to perform metabolome-wide association studies

Description

This function generates bootstrap replicates (non-parametric resampling) of a model testing for association between a given metabolite and a disease phenotype, and calculates the confidence interval of model coefficients. Confidence intervals are calculated using the adjusted bootstrap percentile (BCa) method.

Usage

MWAS_bootstrapping (metabo_SE, metabolite_id, disease_id, confounder_ids = NULL,
                    assoc_method, iterations = 10000)

Arguments

metabo_SE	SummarizedExperiment object. See "MWAS_SummarizedExperiment()".
metabolite_id	character vector corresponding to the id of the metabolite to be modeled.
disease_id	character vector corresponding to the id of the response to be modeled.
confounder_ids	optional character vector corresponding to the ids of covariates to be included in the model (e.g. age or gender).
assoc_method	character constant indicating the association method that will be used. Possible values for assoc_method are: "pearson" (pearson correlation), "spearman" (spearman correlation), "kendall" (kendall correlation), "linear" (linear regression) or "logistic" (logistic regression).
iterations	numeric value indicating the number of bootstrap replicates

Value

A list with 3 elements, each list element reporting the following information: i) object of class "boot"; ii) summary of the previous object; iii) 95-confidence interval of the metabolite model coefficient. For more details, check the function "boot()" from the "boot" package.

References

Davison AC, Hinkley, DV. (1997). Bootstrap Methods and Their Application. Cambridge University Press.

Examples

## Load data
data(targetMetabo_SE)

## Bootstrap model testing for association between diabetes (T2D) and 3OH-butyrate
MWAS_bootstrapping (targetMetabo_SE, metabolite_id = "3-Hydroxybutyrate",
                    disease_id = "T2D",assoc_method = "logistic",
                    iterations = 1000)

MWASTools documentation built on Nov. 8, 2020, 5:07 p.m.