picrust: Predict OTU functional content via PICRUSt

Description

Given an OTU abundance table prepared with the GreenGenes reference database, this function predicts the functional content using either COG or KO precalculated mapping tables that map the taxonomic abundance for a given OTU to functional abundance content across a set of functional genes.

Usage

picrust(
  otu_table,
  rows_are_taxa,
  reference = c("gg_ko", "gg_cog"),
  reference_path,
  cn_normalize = FALSE,
  sample_normalize = FALSE,
  drop = TRUE
)

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).

reference

A string for either gg_ko or gg_cog. Defaults to gg_ko.

reference_path

Folder path of the reference file

cn_normalize

Logical flag for performing 16S rRNA copy number normalization. Defaults to FALSE.

sample_normalize

Logical flag to normalize functional predictions by the total functional abundance in a sample. Defaults to FALSE.

drop

Logical flag to drop empty gene columns. Defaults to TRUE.

Value

A list containing

fxn_table: A matrix of gene counts across topics.
fxn_meta: A list of functional metadata corresponding to fxn_table.
method_meta: A matrix of method specific metadata (NSTI).

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

Run this code

# NOT RUN {
download_ref(destination='/references',reference='gg_ko')

predicted_functions <- picrust(otu_table=GEVERS$OTU,rows_are_taxa=TRUE,
                               reference='gg_ko',reference_path='/references',
                               cn_normalize=TRUE,
                               sample_normalize=FALSE,drop=TRUE)
                           
# }
# NOT RUN {
# }