Clean up the taxonomic table to make taxonomic assignments consistent.
tidy_taxonomy(
taxonomy_table,
column = "all",
pattern = c(".*unassigned.*", ".*uncultur.*", ".*unknown.*", ".*unidentif.*",
".*unclassified.*", ".*No blast hit.*", ".*Incertae.sedis.*"),
replacement = "",
ignore.case = TRUE,
na_fill = ""
)
data.frame
data.frame
object.
a data.frame with taxonomic information (rows are features; columns are taxonomic levels);
or a microtable object with tax_table
in it.
default "all"; "all" or a number; 'all' represents cleaning up all the columns; a number represents cleaning up this specific column.
default c(".*unassigned.*", ".*uncultur.*", ".*unknown.*", ".*unidentif.*", ".*unclassified.*", ".*No blast hit.*", ".*Incertae.sedis.*");
the characters (regular expressions) to be removed or replaced; removed when parameter replacement = ""
,
replaced when parameter replacement has something; Note that the capital and small letters are not distinguished when ignore.case = TRUE
.
default ""; the characters used to replace the character in pattern
parameter.
default TRUE; if FALSE, the pattern matching is case sensitive and if TRUE, case is ignored during matching.
default ""; used to replace NA
.
data("taxonomy_table_16S")
tidy_taxonomy(taxonomy_table_16S)
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