getMetaSignatures: Obtain meta-signatures for a column of interest

In waldronlab/bugsigdbr: R-side access to published microbial signatures from BugSigDB

Obtain meta-signatures for a column of interest

Description

Functionality for obtaining meta-signatures for a column of interest

Usage

getMetaSignatures(
  df,
  column,
  direction = c("BOTH", "UP", "DOWN"),
  min.studies = 2,
  min.taxa = 5,
  comb.fun = sum,
  ...
)

Arguments

df	data.frame storing BugSigDB data. Typically obtained via importBugSigDB.
column	character. Column of interest. Need to be a valid column name of df.
direction	character. Indicates direction of abundance change for signatures to be included in the computation of meta-signatures. Use "UP" to restrict computation to signatures with increased abundance in the exposed group. Use "DOWN" to restrict to signatures with decreased abundance in the exposed group. Defaults to "BOTH" which will not filter signatures by direction of abundance change.
min.studies	integer. Minimum number of studies for a category in column to be included. Defaults to 2, which will then only compute meta-signatures for categories investigated by at least two studies.
min.taxa	integer. Minimum size for meta-signatures. Defaults to 5, which will then only include meta-signatures containing at least 5 taxa.
comb.fun	function. Function for combining sample size of the exposed group and sample size of the unexposed group into an overall study sample size. Defaults to sum which will simply add sample sizes of exposed and unexposed group.
...	additionals argument passed on to getSignatures.

Value

A list of meta-signatures, each meta-signature being a named numeric vector. Names are the taxa of the meta-signature, numeric values correspond to sample size weights associated with each taxon.

See Also

getSignatures

Examples

 df <- importBugSigDB()

 # Body-site specific meta-signatures composed from signatures reported as both 
 # increased or decreased across all conditions of study:
 bs.meta.sigs <- getMetaSignatures(df, column = "Body site")

 # Condition-specific meta-signatures from fecal samples, increased
 # in conditions of study. Use taxonomic names instead of the default NCBI IDs:
 df.feces <- df[df$`Body site` == "Feces", ]
 cond.meta.sigs <- getMetaSignatures(df.feces, column = "Condition", 
                                     direction = "UP", tax.id.type = "taxname")

 # Inspect the results
 names(cond.meta.sigs)
 cond.meta.sigs["Bipolar disorder"]

waldronlab/bugsigdbr documentation built on Oct. 31, 2024, 3:43 a.m.