ancomloop: ANCOM-BC analysis for multiple groups

In nuriamw/micro4all: Microbiome for all

ANCOM-BC analysis for multiple groups

Description

This function is a wrapper of ancombc. When having multiple groups to compare, it allows the user to automatically loop over them and computes all possible combinations. Along with ancombc results, it appends to each table the taxonomy classification.

Usage

ancomloop(
  input_object_phyloseq,
  grouping,
  ancom.options,
  out.unclassified = FALSE,
  tax.level = NULL
)

Arguments

input_object_phyloseq	phyloseq-class. For more details, check distance function.
grouping	Character string. This is used as metadata variable for reordering factors (which allows the function to loop over groups). It is also passed to group and formula arguments in ancombc function.
ancom.options	Further arguments to be passed to ancombc. They should be included as a list (see more information in examples)
out.unclassified	Whether to filter out unclassified taxa (taxa level indicated with argument tax.level). Default is FALSE
tax.level	Character string. Must be a value from 'taxonomyRanks(). Indicates at which level taxa should be filtered out if are unclassified and at which taxonomical level ANCOMBC will be applied.

Value

Returns a list with as many arguments as groups are contained in metadata "grouping" variable. Each element is named after the group which is compared with all others and correspond to a data frame that includes ancombc parameters and the bias-adjusted abundance. In the process, it prints the groups that are being compared (first group against others).

Examples

ancom_location<- ancomloop(location_phyloseq,grouping="location",
ancom.options=list(p_adj_method ="holm", n_cl=4),
out.unclassified=TRUE, tax.level="Genus")

nuriamw/micro4all documentation built on May 2, 2024, 9:18 a.m.