make_comparisons: Make Multiple Comparisons on Transformed Data

In jfq3/QsRutils: R Functions Useful for Community Ecology

Description

Makes multiple comparisons of the relative abundances of taxa between treatment groups using the pairwise.t.test. Data may be transformed by a user supplied function. Three are included in this package.

Usage

make_comparisons(
  expt,
  taxrank = "Phylum",
  grps = "Treatment",
  transformation = "none",
  pc.filter = 0.01,
  p.adjust.method = "BH",
  pool.sd = FALSE
)

Arguments

expt	Experiment level phyloseq object.
taxrank	Rank for which to make comparisons.
grps	Factor in sample data for which to make comparisons.
transformation	Transformation function to use.
pc.filter	Minimum percentage of total counts to include rank in result.
p.adjust.method	Adjustment method for multiple comparisons.
pool.sd	Logical, whether or not to pool standard deviations.

Details

transformation may be "none" or a user-supplied function name in quotation marks or any of the built-it transformations ("arc_sine", "log_arc_sine", or "sqrt_arc_sine"). The "sqrt_arc_sine" has generaally proven most effective.

Value

A data frame with taxa as rows and results in columns.

See Also

arc_sine, log_arc_sine, sqrt_arc_sine, check_var

jfq3/QsRutils documentation built on Jan. 18, 2021, 12:40 a.m.