CatFun: CatFun Function frequency and lineage contribution based...

In genotyper/FunkyTax: Metagenome Functional and Taxonomic Relationships

Description

CatFun takes the results of DESeq2 (Love et al. 2014) and of TaFuR FunkyTax to categorize functions as conserved, equivalent, divergent, or enhanced following Phillips et al. (submitted). These categories describe how differences in metagenome functional repetoire between two or more factor levels relate to differences in underlying microbiome community structure.

Usage

CatFun(tf, ds, alpha = 0.05)

Arguments

tf	Output of TaFuR, which is a list of length five.
ds	Results of DESeq2::results.
alpha	P-value threshold to be applied to Benjamini-Hochberg (Benjamini and Hochberg 1956) adjusted p-values for both DESeq2 and TAFuR analysis. This threshold determines boundaries for function classification.

Value

Output is a list of two with the following:

1:	ggplot object summarizing classification.
2:	Data frame with each function rank-ordered according to abundance and with functional classifications provided.

Author(s)

Caleb D. Phillips

References

Benjamini Y, Hochberg, Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society, Series B. 57:289–300.

Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biology, 15:550.

Phillips CD, Hanson J, Wilkinson J, Koenig L, Rees E, Webala P, Kingston T (submitted) Microbiome Structural and Functional Incongruence Explained along Host Dietary Niche Space. ~

Examples

data(dds)
data(func_dat)
data(met)
a = TaFuR(func_dat, met)
b = CatFun(a, dds)

#renders plot

b[[1]]

genotyper/FunkyTax documentation built on May 17, 2019, 1:11 a.m.