View source: R/misc_analyses.R
core_taxa | R Documentation |
This function returns a data frame with taxa that are determined to be common across multiple sample types based on default or user defined thresholds.
core_taxa(input, type_header, prop_types = 1, prop_reps = 0.5)
input |
The input dataset as loaded by |
type_header |
Mapping file header (in quotation marks) of factor for which you are testing for differences. |
prop_types |
[OPTIONAL] The proportion of sample types in which a taxon must be present to be considered core. |
prop_reps |
[OPTIONAL] The proportion of replicate samples within a sample type in which a taxon must be present to be considered core. |
A data frame with each core taxon as a row. The proportion of sample types where the taxon was present, the mean count of each sample type, and the corresponding taxonomy (if provided), are also returned.
# taxa core to fruits and vegetables core_taxa(fruits_veggies, type_header = 'Sample_type') # relax the proportion of produce/sample types core_taxa(fruits_veggies, type_header = 'Sample_type', prop_types = 0.6)
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