combine.OTU: Combine Non Overlapped OTU tables From The Same Community

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

Description

This function combines otu tables from the same community but based on independent sequencing runs. Such combined otu table gives a more complete profile of the microbial community than each individual otu table does. This function should NOT be used to combine ITS1 and ITS2 otu tables if they were extracted from long NGS sequences.

Usage

combine.OTU(data, meta)

Arguments

data	a list of otu tables to be combined.
meta	the metadata that should have the same number and order of the samples as the otu tables do.

Value

combine.OTU returns a data frame of combined otu tables which have the same samples. Samples in the output will match those in the metadata provided.

Author(s)

Wen Chen

See Also

match.data

Examples

data(ITS1, ITS2, meta)
meta.new <- head(meta)
## Not run: 
# for demonstration purposes only, Not recommend to combine
# ITS1 and ITS2 otu tables that both regions were extracted from
# long NGS sequences
comb <- combine.OTU(data=list(ITS1=ITS1, ITS2=ITS2), meta=meta.new)
stopifnot(identical(colnames(comb)[1:(ncol(comb)-1)],
                    rownames(meta.new)))

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-2
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied

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