taxa.env.correlation: Taxa-Environment correlation

In umerijaz/microbiomeSeq: Microbial community analysis in an environmental context.

Description

This function finds the relationship between most abundant taxa and numerical environmental variables based on correlation. The abundance of each feature/taxa is correlated with each of the environmental variables. A correlation test is performed and associated p-values are adjusted for multiple testing. The scheme of adjustment is elaborated in the arguments section. The function returns a data.frame with raw p-values, corrected p-values, and correlation results.

Usage

taxa.env.correlation(physeq, grouping_column, method = "pearson",
  pvalue.threshold = 0.05, padjust.method = "BH", adjustment = 1,
  num.taxa = 50, select.variables = NULL)

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.
grouping_column	(Required). Character string specifying name of a categorical variable that is preffered for grouping the information. information, this should be one of the components of grouping vector.
method	A character string indicating which correlation coefficient is to be computed, available options are "pearson" which is also the default, "kendall" and "spearman".
adjustment	(optional). An integer to specify how the p-values should be adjusted; 1 - donot adjust 2 - adjust environmental variables + Groups (column on the correlation plot) 3 - adjust Taxa + Groups (row on the correlation plot for each Groups) 4 - adjust Taxa (row on the correlation plot) 5 - adjust environmental variables (panel on the correlation plot)
select.variables	(optional). Character string for the names(s) of environmental variables to be considered in correlation compution. if not given, all numerical variables are considered.
pvalue.threshold.	Cut off p-value for significance of correlation between taxa abundance and environmental variables, default is 0.05.
padjust.method.	Method for adjusting p-values.

Value

A data.frame of correlation results.

Author(s)

Alfred Ssekagiri [e-mail], Umer Zeeshan Ijaz [e-mail]

References

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

Examples

data(pitlatrine)
physeq <- pitlatrine
physeq <- taxa_level(physeq, "Phylum")
tax_env_cor <- taxa.env.correlation(physeq,"Country")
plot_taxa_env(tax_env_cor)

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