otuSummary (version 0.1.1)

subOTU: Subset a OTU table

Description

This function subset a OTU table according to the specified threshold of mean relative abundance.

Usage

subOTU(otutab, siteInCol = TRUE, taxhead = NULL, percent = TRUE, choose = "rare",
       threshold = 1, outype = "Relabund", sort = TRUE, write = FALSE)

Value

This function will return an OTU table (data frame) according to the specified arguments.

Arguments

otutab

An OTU table of microbial community, which can contain a taxonomic column (if siteInCol) or row (if site in rows). The OTU table can be given in numeric counts or in relative abundance.

siteInCol

Logical, if "TRUE", the OTU table contains samples in columns and taxa in rows. The function will decide whether to transpose the OTU table based on this parameter.

taxhead

Character, specify the header of taxonomy. By default the taxonomic column is NULL.

percent

Logical, whether the input OTU table is in relative abundance. The default is TRUE.

choose

Character, tell the function which part to subset out. The valid choice are "rare","abundant" and "all", which will specify the rare biosphere, the abundant population and keep the whole community data.

threshold

Numeric, the threshold specify the relative abundance cutoff upon which the rare biosphere is subset.

outype

Character, specify whether the output otu subset should in relative abundance (outype="Relabund" or "relabund") or in absolute counts (outype="counts" or "Counts"). This function also support partial match of the parameter.

sort

Logical, be default, the output OTU subset is sorted according to the descending order of mean relative abundance across samples.

write

Logical, whether the output OTU table will be written out when running this function. The default is FALSE.

Author

Sizhong Yang <[e-mail]>

Details

The function will subset the OTU table to abundant (choose = "abundant") or rare biosphere (choose = "rare") according to the given relative abundance threshold of rare biosphere (Lynch and Neufeld, 2015). It will also keep the whole community without subsetting, if choose = "all". The output could be relative abundance (outype = "Relabund") or absolute counts (outype = "counts"). If sort is TRUE, the output result will be sorted by the descending order of mean relative abundance across samples.

References

Lynch MDJ, Neufeld JD (2015). Ecology and exploration of the rare biosphere. Nature Reviews Microbiology 13: 217-229.

Examples

data(otuqiime)

example1 <- subOTU(otutab = otuqiime, siteInCol = TRUE, taxhead ="taxonomy",
    percent = FALSE, choose = "abundant", threshold = 1, outype = "Relabund")
dim(example1)

example2 <- subOTU(otutab = otuqiime[,-454], siteInCol = TRUE, taxhead = NULL,
    percent = FALSE, choose = "rare", threshold = 1, outype = "counts")
dim(example2)