preprocess_com: Preprocess Community Data

In jgmv/comecol: Community Ecology Analysis

Preprocess Community Data

Description

Performs preprocessing tasks in community data, removing samples and species with few observations, and normalizing abundance data.

Usage

preprocess_com(
  com,
  min_obs = 100,
  min_taxa = 5,
  normalize = T,
  method = "blind",
  sharingMode = "maximum",
  fitType = "local",
  ...
)

Arguments

com	a community data object.
min_obs	remove samples with a total number of observations below this treshold.
min_taxa	remove species with a total number of observations below this treshold.
normalize	logical, whether to normalize abundances using a mixture model with DESeq.
method	arguments to be passed to 'estimateDispersions'.
sharingMode	arguments to be passed to 'estimateDispersions'.
fitType	arguments to be passed to 'estimateDispersions'.
...	further arguments to be passed to 'estimateDispersions'.

Value

A list with community data.

Examples

preprocess_com.com()

jgmv/comecol documentation built on June 6, 2023, 4:07 p.m.