amp_export_otutable: Export OTU-table

In MadsAlbertsen/ampvis2: Tools for visualising amplicon data

Export OTU-table

Description

Export otutable (including taxonomy) from an ampvis2 object as CSV using write.table.

Usage

amp_export_otutable(
  data,
  filename = "exported_otutable",
  extension = "csv",
  md5 = FALSE,
  sep = "\t",
  id = NULL,
  sort_samples = NULL,
  normalise = FALSE,
  ...
)

Arguments

data	(required) Data list as loaded with amp_load.
filename	File name of the exported OTU-table (excluding extension). (default: "exported_otutable")
extension	File extension (without "."). (default: "csv")
md5	(logical) Compute md5 sum of the data (the whole R-object, not just otutable) and append to the filename. (default: FALSE)
sep	Separator passed directly to fwrite. (default: "\t")
id	Name the samples using a variable in the metadata.
sort_samples	Vector to sort the samples by.
normalise	(logical) Transform the OTU read counts to be in percent per sample. (default: FALSE)
...	Additional arguments passed on to fwrite (other than sep).

Author(s)

Kasper Skytte Andersen [e-mail]

Mads Albertsen [e-mail]

Examples

# Load example data
data("AalborgWWTPs")

# Export OTU-table
## Not run: 
amp_export_otutable(AalborgWWTPs, md5 = TRUE, filename = "AalborgWWTPs_otutable", sep = "\\t")

## End(Not run)

MadsAlbertsen/ampvis2 documentation built on May 21, 2024, 2:11 p.m.