LorMe (version 1.1.0)

tax_summary: 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")
)

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.

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.

Author

Wang Ningqi

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
}