empiricalComposition: Use real data to fit an empirical distribution and generate a...

In vllorens/metaester: Simulate metatranscriptomics datasets

Description

empiricalComposition returns a composition matrix with rows as species/genomes and columns as samples (cases or controls). This composition matrix follows an empirical distribution which has been fitted from real metatranscriptomics datasets See References for the origin of the real datasets. This is an internal function and should not be called directly by the user, only internally by the compositionGenomesMetaT function

Usage

empiricalComposition(empiricalSeed = NULL, genomes, nReplicates)

Arguments

empiricalSeed	A single number or a numeric vector of length equal to nReplicates. Indicates the random seed to assign the reads to different species in each sample. If NULL or a single number, the same seed will be applied to all samples so that they will have the same composition, with differences only due to random sampling.
genomes	Character vector of genome names or genome IDs for the genomes to include in the simulation.
nReplicates	A number, indicating the total samples (cases and controls).

Value

A microbial composition matrix of nReplicates columns and nrow(genomes) rows.

References

Martinez X. et al (2016): MetaTrans: an open source pipeline for metatranscriptomics Scientific Reports 6, Article number: 26447

See Also

compositionGenomesMetaT

vllorens/metaester documentation built on April 26, 2020, 6:55 p.m.