Clean up the taxonomic table to make taxonomic assignments consistent.
Clean up the taxonomic table to make taxonomic assignments consistent.
tidy_taxonomy(
taxonomy_table,
column = "all",
pattern = c(".*uncultur.*", ".*unknown.*", ".*unidentif.*", ".*unclassified.*",
".*No blast hit.*", ".*sp\\.$", ".*metagenome.*", ".*cultivar.*", ".*archaeon$",
"__synthetic.*", ".*\\sbacterium$", ".*bacterium\\s.*"),
replacement = "",
ignore.case = TRUE,
na_fill = ""
)taxonomy_table |
a data.frame with taxonomic information. |
column |
default "all"; "all" or a number; 'all' represents cleaning up all the columns; a number represents cleaning up this column. |
pattern |
default see the function parameter; the characters (regular expression) to be cleaned up or replaced; cleaned up when parameter replacement = "", replaced when parameter replacement has something; Note that the capital and small letters are not distinguished. |
replacement |
default ""; the characters used to replace the character in pattern parameter. |
ignore.case |
default TRUE; if FALSE, the pattern matching is case sensitive and if TRUE, case is ignored during matching. |
na_fill |
default ""; used to replace the NA. |
data.frame object.
taxonomic table.
data("taxonomy_table_16S")
tidy_taxonomy(taxonomy_table_16S)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.