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

Description Usage Arguments Value References Examples

View source: R/cnn.R

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

1
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

1
nOTU <- cnn(GEVERS$OTU,rows_are_taxa=FALSE,drop=TRUE)

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