MWAS_bootstrapping: MWAS bootstrap resampling

Description Usage Arguments Value References Examples

View source: R/MWAS_bootstrapping.R

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

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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

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## 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.