tax_summary: Encapsulate meta file, feature tables and taxonomy annotation...

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Encapsulate meta file, feature tables and taxonomy annotation into tax summary object

Description

The function packages meta file, feature tables and taxonomy annotation into tax summary object

Usage

tax_summary(
  groupfile,
  inputtable,
  reads = TRUE,
  taxonomytable,
  into = "standard",
  sep = ";",
  outputtax = c("Phylum", "Genus")
)

Arguments

groupfile	A data frame containing treatment information
inputtable	OTU/ASV/species data frame with all numeric. Samples ID should be in column names.
reads	Logical.True for reads table and FALSE for percentage table. Default: TRUE
taxonomytable	Taxonomy annotation data frame,with first column OTU/ASV/TAX number ID and second column taxonomy annotation. See details in example.
into	Names of separated taxonomy to create as character vector. Must select from c("Domain","Phylum","Class","Order","Family","Genus","Species"). Shortcut input:1)By default."standard":c("Domain","Phylum","Class","Order","Family","Genus","Species"). Used for standard taxonomy annotation to OTU/ASV table. 2)"complete":c("Domain","Kingdom","Phylum","Class","Order","Family","Genus","Species"). Used for complete taxonomy annotation to meta genomic table.
sep	Separator of taxonomy table.Default: ";".
outputtax	Names of output taxonomy level table. Default:c("Phylum","Genus"). Shortcut input is available with 'standard' and 'complete' same as above.

Value

One list containing taxonomy table data frame,containing reads and percentage table for each specified output. Full taxonomy annotation data frame is output in global environment.

Note

For taxonomy annotation with 'Kingdom' level, please set 'into' parameter as 'complete'!!!

Author(s)

Wang Ningqi [e-mail]

Examples

{
  # Load data
  data(testotu)

  # Create group information data frame
  groupinformation <- data.frame(
    group = c(rep("a", 10), rep("b", 10)),
    factor1 = rnorm(10),
    factor2 = rnorm(mean = 100, 10),
    subject = factor(c(1:10, 1:10))
  )

  # Packaging data into a taxonomy summary object
  test_object <- tax_summary(
    groupfile = groupinformation,
    inputtable = testotu[, 2:21],
    reads = TRUE,
    taxonomytable = testotu[, c(1, 22)]
  )

  # Check integrated object
  print(test_object)

  # Extract genus relative abundance table
  test_Genus <- test_object$Genus_percent
  head(test_Genus)

  # Check corresponding taxonomy information of genus table
  test_Genus_tax <- test_object$Genus_taxonomy
  head(test_Genus_tax)

  # Summary base table into all taxonomy levels with standard output
  test_object <- tax_summary(
    groupfile = groupinformation,
    inputtable = testotu[, 2:21],
    reads = TRUE,
    taxonomytable = testotu[, c(1, 22)],
    outputtax = "standard"
  )
  head(test_object$Species_percent)  # View first 10 rows of species percentage
  head(test_object$Genus)  # View first 10 rows of genus table
}

LorMe documentation built on Sept. 13, 2024, 9:07 a.m.