KDA: kernel-based differential analysis

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

Description

This function performs differential analysis using a distance-based kernel score test. It obtains set(s) of differentially abundant features between a specified pair of conditions/groups. The sets are obtained by grouping based on correlation of abundance among features. The strength of the relationship that must exist for features/variables to belong to the same set can be specified. A similar approach applies to environmental variables which can also be grouped into sets depending on a desired level of correlation amongst member variables.

Usage

KDA(physeq, grouping_column, analyse = "abundance", method = "dscore",
  p.adjust.method = "BH", corr = 0.99,
  adjusted.p.value.threshold = 0.05, 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, this should be one of the components of grouping vector.
analyse	(optional). A character string specifying whether to analyse taxa abundance ("abundance") or sample data ("meta"). Default is set to analyse taxa abundance.
method	(optional). A character string specifying the kernel based method to be used for differential analysis, two options are available for this; "dscore" and "sscore". See dscore and sscore for details.
p.adjust.method	(optional). method to adjust raw pvalues obtained by the distance based score tests.
corr	(optional). Threshold correlation on which grouping of features/ variables is based.
adjusted.p.value.threshold	Cut off p-value for significance of differentially abundant/correlated taxa/environmental variables, default is 0.05.

Value

Returns a list of two items:

• kscore_table: A data.frame of taxa/ environmental variable with kernel based score stats, raw and adjusted pvalues.

• plotdata: A data.frame similar to kcore_table but organised in a way compatible to ggplot.

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<-data(pitlatrine)
physeq<- taxa_level(physeq, "Phylum")
kda_sig  <- KDA(physeq,grouping_column = "Country")
plot_kda(kda_sig$plotdata)

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