shared.Taxa: Summary of Shared Taxa Across ALL Subjects

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function consumes OTU tables or a taxonomy matrices and returns a list summarizing information about the presence of the taxa in that table at a given taxonomic rank.

Usage

shared.Taxa(data, is.OTU=TRUE, rank="g")

Arguments

data	a list of OTU tables or taxonomy abundance matrices.
is.OTU	whether or not the input data are otu tables
rank	the taxonomic rank to be investigated

Value

shared.Taxa returns a list containing the information calculated. The names associated with the list describe what that number represents; i.e. "#_of_families_in_all_samples" shows how many taxa at the family level were found to be present in all samples. The last item in the list is a character vector, containing the taxon names of which were present in all samples.

Note

The taxa are determined to be absent/present using the "pa" method from the function decostand.

Author(s)

Wen Chen.

See Also

decostand

Examples

data(ITS1)
shared.Taxa(data=list(ITS1=ITS1))
## Not run: 
g1 <- tax.abund(ITS1, rank="g", drop.unclassified=TRUE)
shared.Taxa(data=list(genus_ITS1=g1), rank="g", is.OTU=FALSE)

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
$ITS1
$ITS1$`#_of_genera_in_1_sample`
[1] 23

$ITS1$`#_of_genera_in_>1_sample`
[1] 48

$ITS1$`#_of_genera_in_all_samples`
[1] 11

$ITS1$`%_of_genera_in_one_sample`
[1] 0.3239437

$ITS1$`%_of_genera_in_all_samples`
[1] 0.1549296

$ITS1$`#_of_sequence_in_shared_genera`
[1] 180002

$ITS1$`%_of_sequence_in_shared_genera`
[1] 0.6232411

$ITS1$genera_in_all_samples
 [1] "Fusarium"       "Cryptococcus"   "Alternaria"     "Cladosporium"  
 [5] "Sporobolomyces" "Aureobasidium"  "Epicoccum"      "Rhodotorula"   
 [9] "Pleospora"      "Pyrenophora"    "Phaeosphaeria" 


$genus_ITS1
$genus_ITS1$`#_of_taxa_in_1_sample`
[1] 23

$genus_ITS1$`#_of_taxa_in_>1_sample`
[1] 48

$genus_ITS1$`#_of_taxa_in_all_samples`
[1] 11

$genus_ITS1$`%_of_taxa_in_one_sample`
[1] 0.3239437

$genus_ITS1$`%_of_taxa_in_all_samples`
[1] 0.1549296

$genus_ITS1$`#_of_sequence_in_shared_taxa`
[1] 180002

$genus_ITS1$`%_of_sequence_in_shared_taxa`
[1] 0.9868964

$genus_ITS1$taxa_in_all_samples
 [1] "Fusarium"       "Cryptococcus"   "Alternaria"     "Cladosporium"  
 [5] "Sporobolomyces" "Aureobasidium"  "Epicoccum"      "Rhodotorula"   
 [9] "Pleospora"      "Pyrenophora"    "Phaeosphaeria" 


Warning message:
In shared.Taxa(data = list(genus_ITS1 = g1), rank = "g", is.OTU = FALSE) :
  data are not otu tables, will ignore the rank provided

RAM documentation built on May 2, 2019, 3:04 p.m.