testReplicability: Test replicability of microbiome changes across studies

In waldronlab/BugSigDBStats: BugSigDB Stats and Analysis

Test replicability of microbiome changes across studies

Description

Function that implements a statistical test for replicability of microbiome changes for experimental conditions in BugSigDB

Usage

testReplicability(
  df,
  onto = NULL,
  multi.contrast = c("all", "first", "largest", "merge"),
  min.studies = 2,
  min.taxa = 5
)

Arguments

df	data.frame storing BugSigDB data. Typically obtained via importBugSigDB.
onto	ontology. An object of class ontology_index storing the NCBI Taxonomy. Typically obtained via getNcbiTaxonomyObo.
multi.contrast	character. How to treat studies that report multiple contrasts for a study to avoid detection of duplication within studies as replication? Select one of "all" incorporates all contrasts reported by a study. This is equivalent to do nothing, ie computes similarity between signatures taking all, and thus potential similar / duplicated, signatures for each study into account. "first" take only the first contrast reported by a study, ie the first signature with increased abundance and the first signature with decreased abundance in the study group. "largest" take only the largest signature with increased and decreased abundance in the study group, respectively. "merge" merge signatures with the same direction of abundance change (increased or decreased) within studies.
min.studies	integer. Minimum number of studies for a condition to be tested. Defaults to 2, which will then only test a condition investigated by at least two studies.
min.taxa	integer. Minimum size for a signature to be included. Defaults to 5, which will then only include signatures containing at least 5 taxa.

Value

A data.frame reporting semantic similarity and re-sampling p-value for each condition under investigation. Results are stratified by direction of abundance change in the study group.

Examples

 dat <- bugsigdbr::importBugSigDB(version = "10.5281/zenodo.5904281")
 dat.feces <- subset(dat, `Body site` == "feces")
 res <- testReplicability(dat.feces)

waldronlab/BugSigDBStats documentation built on Oct. 15, 2024, 5:16 p.m.