cnn: Normalize an OTU table by 16S rRNA copy number
Description
Implements 16S rRNA copy number normalization using the PICRUSt 16S
GreenGreenes 13.5 copy number count table (default) or a user provided set of
copy numbers.
Usage
cnn(otu_table, rows_are_taxa, copy_numbers, drop = TRUE, verbose = FALSE)
Arguments
otu_table
(required) Matrix or dataframe containing taxa abundances
(counts, non-negative integers) across samples. Rows and columns must be
uniquely named.
rows_are_taxa
(required) Logical flag indicating whether otu_table
rows correspond to taxa (TRUE) or samples (FALSE).
copy_numbers
A 2-column matrix or data frame of copy numbers where
column 1 contains the OTU IDs and column 2 the copy numbers.
drop
Logical flag to drop empty rows and columns. Defaults to TRUE.
verbose
Logical flag to print progress information. Defaults to FALSE.
Value
A normalized, rounded (to nearest integer) abundance table.
References
Langille, M. G.I.*, Zaneveld, J.*, Caporaso, J. G., McDonald, D., Knights, D.,
a Reyes, J., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R.,
Beiko, R. G., and Huttenhower, C. (2013). Nature Biotechnology, 1-10. 8.