retain.resolve_genus | R Documentation |
Execute retain-resolve agglomeration on ASV count data stored in phyloseq object.
Filter are required for at the ASV and genus-level for:
mean relative abundance + prevalence
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.
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 )
physeq |
input phyloseq object containing taxa counts |
dir |
Input filepath as string for storage location of exported files if export = |
export |
|
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: |
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: |
prev.genus |
threshold for prevalence filter for agglomerated genus-level taxa to be retained. Input numeric value. Default is 0.5 prevalence. |
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 )
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
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