tidy_taxonomy {microeco} | R Documentation |
Clean up the taxonomic table to make taxonomic assignments consistent.
Description
Clean up the taxonomic table to make taxonomic assignments consistent.
Usage
tidy_taxonomy(
taxonomy_table,
column = "all",
pattern = c(".*unassigned.*", ".*uncultur.*", ".*unknown.*", ".*unidentif.*",
".*unclassified.*", ".*No blast hit.*", ".*Incertae.sedis.*"),
replacement = "",
ignore.case = TRUE,
na_fill = ""
)
Arguments
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 c(".*unassigned.*", ".*uncultur.*", ".*unknown.*", ".*unidentif.*", ".*unclassified.*", ".*No blast hit.*", ".*Incertae.sedis.*");
the characters (regular expressions) to be removed or replaced; removed when parameter |
replacement |
default ""; the characters used to replace the character in |
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 |
Format
data.frame
object.
Value
data.frame
Examples
data("taxonomy_table_16S")
tidy_taxonomy(taxonomy_table_16S)