split_assignments: Split taxonomic assignment strings

In qiimer: Work with QIIME Output Files in R

Description

Split taxonomic assignment strings

Usage

split_assignments(assignments, ranks = taxonomic_ranks, split = "; ", ...)

Arguments

assignments	Character vector of taxonomic assignments.
ranks	Character vector of taxonomic ranks, used as column names in the resultant data frame.
split	Pattern on which to split taxa in assignment strings.
...	Additional parameters are passed to the strsplit function.

Value

A data frame of taxonomic assignments.

See Also

taxonomic_ranks

Examples

data(relmbeta_assignments)
a <- split_assignments(relmbeta_assignments)
head(a)

Example output

          Kingdom        Phylum      Class         Order          Family Genus
denovo0  Bacteria    Firmicutes Clostridia Clostridiales            <NA>  <NA>
denovo1  Bacteria    Firmicutes Clostridia Clostridiales            <NA>  <NA>
denovo2  Bacteria    Firmicutes Clostridia          <NA>            <NA>  <NA>
denovo6  Bacteria Bacteroidetes       <NA>          <NA>            <NA>  <NA>
denovo9  Bacteria    Firmicutes Clostridia Clostridiales Lachnospiraceae  <NA>
denovo16 Bacteria    Firmicutes       <NA>          <NA>            <NA>  <NA>

qiimer documentation built on May 2, 2019, 6 a.m.