Description Usage Arguments Value
View source: R/miscellaneous.R
Given a phyloseq object with 'otu_table', 'tax_table', 'sam_data' (required) it gives a list with those tables.
1 | get_physeq_tbls(physeq, tax_rank = NULL, rm_na = FALSE, feature_w_tax = FALSE)
|
physeq |
phyloseq-class object with 'otu_table', 'tax_table', 'sam_data' slots (required). |
tax_rank |
taxonomic rank (character). One of the taxonomic ranks among the column names of 'tax_table()' of the 'physeq' object given. |
rm_na |
include (TRUE) or not (FALSE) NAs (logical), i.e., taxa without classification at the taxonomic level specified at 'tax_rank'. It only works if 'tax_rank' was provided. Otherwise it is ignored. |
feature_w_tax |
substitute the feature labels (in columns) by the taxa names specified at 'tax_rank' level (logical). Default is 'FALSE'. It only works if 'tax_rank' was provided. Otherwise it is ignored. |
A list with the 'feature' ('otu_table'), 'taxonomy' ('tax_table'), and 'metadata' ('sample_data') tables. If the 'tax_rank' is specified, it will give 'feature' and 'taxonomy' summarized at that 'tax_rank' level. If 'feature_w_tax' is equal 'TRUE' (only works together with 'tax_rank'), the column names in the 'feature' table will be the taxa names at 'tax_rank' level specied.
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