normalise_data: Data normalisation

Description Usage Arguments Value Author(s) References Examples

Description

This function normalises taxa abundance

Usage

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normalise_data(physeq, norm.method, ...)

Arguments

physeq

(Required). A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.

method

(Required). A method to used to normalise the data. Available methods include: "edgeRnorm", "varstab", "randomsubsample", "proportion" .

Value

Returns a phyloseq object whose abundance data is normalised.

Author(s)

Alfred Ssekagiri assekagiri@gmail.com, Umer Zeeshan Ijaz Umer.Ijaz@glasgow.ac.uk

References

http://userweb.eng.gla.ac.uk/umer.ijaz/, Umer Ijaz, 2015

Examples

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data(pitlatrine)
physeq<-data(pitlatrine)
physeq <- normalise_data(physeq,method = "randomsubsample")
physeq <- normalise_data(physeq,method = "edgeRnorm")
physeq <- normalise_data(physeq,method = "proportion")

umerijaz/microbiomeSeq documentation built on May 30, 2019, 3:13 p.m.