Replace taxonomic value with a given pattern by NA — taxtab_replace_pattern_by

Use base::gsub() for substitution.

Usage

taxtab_replace_pattern_by_NA(
  physeq,
  patterns = c(".*_incertae_sedis", "unclassified.*"),
  taxonomic_ranks = NULL,
  progress_bar = FALSE,
  ...
)

Arguments

physeq: (required) A phyloseq-class object obtained using the phyloseq package.
patterns: (character vector, default c("._incertae_sedis", "unclassified.")) A vector of patterns to select taxonomic values to convert to NA.
taxonomic_ranks: (character vector, default NULL) A vector of taxonomic ranks where the substitution should occur. If left to NULL, all taxonomic ranks are modified.
progress_bar: (logical, default FALSE) If TRUE, print progress during the calculation.
...: Additional arguments passed to base::gsub().

Value

A phyloseq object

Author

Adrien Taudière

Examples

data_fungi@tax_table["ASV85", "Family"]
#> Taxonomy Table:     [1 taxa by 1 taxonomic ranks]:
#>       Family                              
#> ASV85 "Hymenochaetales_fam_Incertae_sedis"
data_fungi2 <- taxtab_replace_pattern_by_NA(data_fungi, "fam_Incertae_sedis", taxonomic_ranks = "Family")
data_fungi2@tax_table["ASV85", "Family"]
#> Taxonomy Table:     [1 taxa by 1 taxonomic ranks]:
#>       Family
#> ASV85 NA    

# By default patterns ".*_incertae_sedis" and "unclassified.*" are replaced by NA
data_fungi3 <-
  taxtab_replace_pattern_by_NA(data_fungi, ignore.case = TRUE, progress_bar = TRUE)
#> 
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data_fungi3@tax_table["ASV85", "Family"]
#> Taxonomy Table:     [1 taxa by 1 taxonomic ranks]:
#>       Family
#> ASV85 NA