retain.resolve_genus: Retain resolve agglomeration

In SarahAsbury/retainresolve: Retain Resolve Microbiome Agglomeration

Retain resolve agglomeration

Description

Execute retain-resolve agglomeration on ASV count data stored in phyloseq object.

Filter are required for at the ASV and genus-level for:

1. mean relative abundance + prevalence

2. prevalence only

Users wishing to set thresholds for only one criteria (e.g mra + prev or prev only) can set the parameters for the unused filter to 0. Thresholds for ASV and genus-level filtering may need to be optimized for each dataset using summary plots exported when export = TRUE.

Exporting quality control data to file (export = TRUE) is highly recommend.

Usage

retain.resolve_genus(
  physeq,
  dir = NA,
  export,
  mra_prev.ASV = c(0.001, 0.1),
  prev.ASV = 0.5,
  mra_prev.genus = c(1e-04, 0.1),
  prev.genus = 0.5
)

Arguments

physeq	input phyloseq object containing taxa counts
dir	Input filepath as string for storage location of exported files if export = TRUE.
export	TRUE or FALSE. If TRUE, quality control data and additional phyloseq objects will be exported to a specified directory.
mra_prev.ASV	threshold for mean relative abundance + prevalence filter. Both minimum values must be met for ASV taxa to be retained. Input numeric vector: c(mra, prev). Default is 0.001 mean relative abundance and 0.1 prevalence.
prev.ASV	threshold for prevalence filter for ASV to be retained. Input numeric value. Default is 0.5 prevalence.
mra_prev.genus	threshold for mean relative abundance + prevalence filter. Both minimum values must be met for agglomerated genus-level taxa to be retained. Input numeric vector: c(mra, prev). Default is 0.0001 mean relative abundance and 0.1 prevalence.
prev.genus	threshold for prevalence filter for agglomerated genus-level taxa to be retained. Input numeric value. Default is 0.5 prevalence.

Value

Phyloseq objects:
dat_glom: retain-resolved ASV and genus-level taxa count data. Other taxa is not included.

dat_glom_aldex: retain-resolved ASV and genus-level taxa count data. Other taxa classification is included such that total abundances are unchanged from original count data after genus-level filtering. Recommended use for downstream applications where calculations use total abundance (e.g CLR transformation, relative abundance).

dat_glom_rel: retain-resolved ASV and genus-level taxa relative abundance data. Calculated with dat_glom_aldex. Other taxa has been removed after relative abundance calculation.


Dataframes:
glom.spID.taxonomt: key for taxonomic level (ASV or genus) of each taxonomic ID (e.g )

Examples

output <- retain.resolve_genus(physeq = dat, export = TRUE, dir = "filepath/export_files") #use default thresholds

output <- retain.resolve_genus(physeq = dat, export = TRUE, dir = "~filepath/export_files", mra_prev.ASV = c(0.005, 0.25), prev.ASV = 0.75, mra_prev.genus = c(0.001, 0.1), prev.genus = 0.5) #manually set thresholds for genus and ASV-level filters

SarahAsbury/retainresolve documentation built on Feb. 20, 2023, 7:48 a.m.