data: Tests if there is a significant difference in abundance...

In MadsAlbertsen/ampvis: Tools for visualising amplicon data

Description

A nice long description

Usage

amp_test(data, group)

Arguments

data	(required) A phyloseq object including sample data.
group	(required) A variable from the associated sample data to group samples by.
tax.aggregate	Group data at specific taxonomic level (defaul: "Genus").
tax.clean	Replace the phylum Proteobacteria with the respective Classes instead (default: T).
tax.empty	Either "remove" OTUs without taxonomic information or "rename" with OTU ID (default: rename).
scale.seq	The number of sequences in the pre-filtered samples (default: 20000)

Format

Formal class 'phyloseq' [package "phyloseq"] with 5 slots
  ..@ otu_table:Formal class 'otu_table' [package "phyloseq"] with 2 slots
  .. .. ..@ .Data        : num [1:380, 1:28] 0 5 0 0 1 0 0 0 0 0 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:380] "denovo38" "denovo256" "denovo394" "denovo433" ...
  .. .. .. .. ..$ : chr [1:28] "16S-AMP-1147" "16S-AMP-1149" "16S-AMP-1156" "16S-AMP-1113" ...
  .. .. ..@ taxa_are_rows: logi TRUE
  ..@ tax_table:Formal class 'taxonomyTable' [package "phyloseq"] with 1 slots
  .. .. ..@ .Data: chr [1:380, 1:6] "k__Bacteria" "k__Bacteria" "k__Bacteria" "k__Bacteria" ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:380] "denovo38" "denovo256" "denovo394" "denovo433" ...
  .. .. .. .. ..$ : chr [1:6] "Kingdom" "Phylum" "Class" "Order" ...
  ..@ sam_data :'data.frame':	28 obs. of  14 variables:
Formal class 'sample_data' [package "phyloseq"] with 4 slots
  .. .. ..@ .Data    :List of 14
  .. .. .. ..$ : Factor w/ 28 levels "16S-AMP-1106",..: 11 13 14 6 21 9 8 12 16 15 ...
  .. .. .. ..$ : Factor w/ 7 levels "Bjergmarken",..: 6 6 2 5 4 1 1 6 2 2 ...
  .. .. .. ..$ : Factor w/ 4 levels "2013-02-04","2013-05-06",..: 2 4 2 1 3 3 2 3 4 3 ...
  .. .. .. ..$ : int [1:28] 2013 2013 2013 2013 2013 2013 2013 2013 2013 2013 ...
  .. .. .. ..$ : Factor w/ 4 levels "Fall","Spring",..: 2 1 2 4 3 3 2 3 1 3 ...
  .. .. .. ..$ : Factor w/ 2 levels "N","Y": 2 2 1 1 1 2 2 2 1 1 ...
  .. .. .. ..$ : Factor w/ 2 levels "N","Y": 1 1 1 2 2 1 1 1 1 1 ...
  .. .. .. ..$ : Factor w/ 1 level "Y": 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ : Factor w/ 2 levels "N","Y": 2 2 2 2 1 2 2 2 2 2 ...
  .. .. .. ..$ : Factor w/ 2 levels "N","Y": 1 1 1 1 2 1 1 1 1 1 ...
  .. .. .. ..$ : Factor w/ 2 levels "N","Y": 2 2 1 1 2 2 2 2 1 1 ...
  .. .. .. ..$ : Factor w/ 5 levels "0.1","0.2","0.3",..: 1 1 4 2 3 2 2 1 4 4 ...
  .. .. .. ..$ : Factor w/ 2 levels "N","Y": 2 2 1 1 2 1 1 2 1 1 ...
  .. .. .. ..$ : Factor w/ 3 levels "Acetic acid and protein",..: 2 2 3 3 1 3 3 2 3 3 ...
  .. .. ..@ names    : chr [1:14] "SampleID" "Plant" "Date" "Year" ...
  .. .. ..@ row.names: chr [1:28] "16S-AMP-1147" "16S-AMP-1149" "16S-AMP-1156" "16S-AMP-1113" ...
  .. .. ..@ .S3Class : chr "data.frame"
  ..@ phy_tree : NULL
  ..@ refseq   : NULL

Value

A p-value for each comparison.

Author(s)

Mads Albertsen [e-mail]

MadsAlbertsen/ampvis documentation built on May 7, 2019, 2:08 p.m.