OTU.subsets: Subset OTU And Metadata

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

Description

This function subset OTUs and metadata based on user defined values of metadata variables.

Usage

data.subset(data, meta, factors="", values="", and=TRUE)

Arguments

data	a list of otu tables to be processed. See also RAM.input.formatting.
meta	the metadata for subset.
factors	a vector containing metadata variables.
values	a vector containing values of interest in metadata variables.
and	logical. Determine whether all conditions needs to be met or not.

Value

The value returned by this function is a list containing otu tables matching the filtering requirement. The last item in the output list is the associated new metadata table fit the requirement.

Author(s)

Wen Chen

Examples

data(ITS1, ITS2, meta)
names(meta)
factors <- c("City", "Harvestmethod")
values <- c("City1", "Method1")
# match all requirements, and=TRUE
sub <- data.subset(data=list(ITS1=ITS1, ITS2=ITS2), meta=meta,
                   factors=factors, values=values, and=TRUE)
# match either of the requirements, and=FALSE
sub <- data.subset(data=list(ITS1=ITS1, ITS2=ITS2), meta=meta,
                   factors=factors, values=values, and=FALSE)
## Not run: 
names(sub)
ITS1.sub <- sub[["ITS1"]]
ITS2.sub <- sub[["ITS2"]]
meta.sub <- sub[["meta"]]

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
 [1] "Sample"         "City"           "Crop"           "Plots"         
 [5] "Harvestmethod"  "Harvestdate"    "Ergosterol_ppm" "Province"      
 [9] "Latitude"       "Longitude"     
[1] "ITS1" "ITS2" "meta"

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