cnn: Normalize an OTU table by 16S rRNA copy number

In EESI/themetagenomics: Exploring Thematic Structure and Predicted Functionality of 16s rRNA Amplicon Data

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.

Examples

nOTU <- cnn(GEVERS$OTU,rows_are_taxa=FALSE,drop=TRUE)

EESI/themetagenomics documentation built on May 10, 2020, 1:40 a.m.