RAM.input.formatting: Data Input Formatting

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

Description

When use some RAM functions for the comparison of multiple OTU tables or taxonomic abundance matrices, the user needs to privde all input data sets as list with names being provided.

one data set:

data=list(data=otu)

multiple data sets:

data=list(data1=otu1, data2=otu2, data3=otu3)

an OTU table:

a data frame of otuIDs x sampleIDs with the last column named "taxonomy"

a taxonomy abundance matrix:

a data frame of sampleIDs x taxa (e.g. species)

is.OTU:

logical, many functions in RAM require the user to set is.OTU to be TRUE for OTU tables or FALSE for a taxonomy abundance matrices.

Author(s)

Wen Chen.

Examples

data(ITS1, ITS2, meta)
# use otu tables
matched <- match.data(data=list(otu_ITS1=ITS1, otu_ITS2=ITS2),
           is.OTU=TRUE, meta=meta)
# taxonomy abundance matrices
g1 <- tax.abund(ITS1, rank="g")
g2 <- tax.abund(ITS2, rank="g")
matched <- match.data(data=list(genus_ITS1=g1, genus_ITS2=g2),
           is.OTU=FALSE, meta=meta)

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

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