t4f: Predict taxonomic functional content via tax4fun

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

Description

Given a taxonomic abundance table prepared with the Silva reference database, predicts the functional content using a KO precalculated mapping table that maps the taxonomic abundance for a given tax_table to functional abundance content across a set of functional genes.

Usage

t4f(
  otu_table,
  rows_are_taxa,
  tax_table,
  reference_path,
  type = c("uproc", "pauda"),
  short = TRUE,
  cn_normalize = FALSE,
  sample_normalize = FALSE,
  scalar,
  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).
tax_table	Matrix or dataframe containing Silva taxonimic information with row or column names corresponding to the otu_table. Silva species information is required.
reference_path	Folder path of the silva-to-kegg mapping file (t4f_silva_to_kegg.rds) and reference profiles (t4f_ref_profiles.rds). Must not be renamed.
type	Type of protein domain classification methods used to generate references (uproc or pauda). Defaults to uproc.
short	Logical flag whether to use a short or long read references. Defaults to TRUE.
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.
scalar	Value for scaling the topics over functions distrubution to predicted counts.
drop	Logical flag to drop empty gene columns after prediction. Defaults to TRUE.
verbose	Logical flag to print progress information. Defaults to FALSE.

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 (FTU).

References

ABhauer, K. P., Wemheuer, B. Daniel, R., and Meinicke, P. (2015). Bioinformatics, 1-3. 31(17).

See Also

download_ref picrust

Examples

## Not run: 
download_ref(destination='/references',reference='silva_ko')
predicted_functions <- t4f(otu_table=DAVID$OTU,rows_are_taxa=FALSE,
                           tax_table=DAVID$TAX,reference='/references',
                           type='uproc',short=TRUE,cn_normalize=TRUE,
                           sample_normalize=FALSE,scalar=NULL,drop=TRUE)
                           
## End(Not run)

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