CombineProjects: Combine taxonomic tables and metadata of two projects

In katrikorpela/mare: Microbiota Analysis in R Easily

Combine taxonomic tables and metadata of two projects

Description

Combines the organised taxonomic tables and metadata files of two projects that were processed separately, and (optionally) removes batch effects (mean-level differences between projects).

Usage

CombineProjects(project1folder,project2folder, meta1, meta2, batch.effect = F, all.taxa = T)

Arguments

project1folder	Path to the folder where data files of project 1 are located.
project2folder	Path to the folder where data files of project 2 are located.
meta1	Name of the metadatafile for project 1.
project1folder	Name of the metadatafile for project 2.
batch.effect	Set to TRUE, if you want to remove a batch effect, i.e. to standardise the mean relative abundances of the taxa.
all.taxa	Set to TRUE, if you want to include all taxa that appear at least in one of the projects. The default (FALSE) includes only taxa that are observed in both projects.

Details

This function combines the organised taxonomic tables and metadata files. The function assumes that the metadata files are in the same project folders (project1folder and project2folder).

Author(s)

Katri Korpela

Examples

## Not run: 
CombineProjects(project1folder="/path/to/project1",
                project2folder="/path/to/project2",
                meta1="meta1.txt",meta2="meta2.txt")


## End(Not run)

katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.