tidyMicro (version 1.43)

otu_filter: A function to aggregate low prevalence, abundance, or unwanted taxa together

Description

Will take a tidi_micro set and aggregate the raw counts of taxa with a low prevalence and/or abundance into a new "Other" taxa. Can also find specific taxa you'd like to include in the "Other" taxa counts. Once the counts are aggregated taxa relative abundance, centered log ratio (CLR) transformations, and presence will be recalculated. This recalculation will only change the "Other" category

Usage

otu_filter(
  micro_set,
  prev_cutoff = 0,
  ra_cutoff = 0,
  exclude_taxa = NULL,
  filter_summary = T
)

Arguments

micro_set

A tidy_micro data set

prev_cutoff

Minimum percent of subjects with OTU counts above 0

ra_cutoff

At leat one subject must have RA above this subject

exclude_taxa

A character vector of OTU names that you would like filter into your "Other" category

filter_summary

Logical; print out summaries of filtering steps

Value

Returns a tidy_micro set

Details

\(\frac{1}{Total}\) will be added to each taxa count for CLR tranformations in order to avoid issues with log(0)

Examples

# NOT RUN {
data(phy); data(cla); data(ord); data(fam); data(clin)

otu_tabs = list(Phylum = phy, Class = cla, Order = ord, Family = fam)
set <- tidy_micro(otu_tabs = otu_tabs, clinical = clin) %>%
filter(day == 7) ## Only including the first week

filter_set <- set %>%
otu_filter(prev_cutoff = 5, ## 5% of subjects must have this bug, or it is filtered
  ra_cutoff = 1, ## At least 1 subject must have RA of 1, or it is filtered
  exclude_taxa = c("Unclassified", "Bacteria") ## Unclassified taxa we don't want
)
# }