read.profiling: read.profiling

In microbiome/microbiomeold: Tools for microbiome analysis

Description

Read run.profiling.script output into R

Usage

read.profiling(level = NULL, method = "frpa", data.dir, log10 = TRUE,
  impute = TRUE)

Arguments

level	phylogenetic level ('oligo' / 'species' / 'L1' / 'L2' / 'L0') or 'phylogeny.full', 'phylogeny.filtered'
method	('frpa' / 'rpa' / 'sum' / 'ave')
data.dir	Profiling script output directory for reading the data. If not given, GUI will ask to specify the file and overruns the possible level / method arguments in the function call.
log10	Logical. Logarithmize the data TRUE/FALSE. By default, the data is in original non-log scale.
impute	impute missing oligo signals

Value

data matrix (phylo x samples)

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation('microbiome')

Examples

data.dir <- system.file("extdata", package = "microbiome")
  dat <- read.profiling('L1', 'frpa', data.dir = data.dir)

microbiome/microbiomeold documentation built on May 22, 2019, 9:57 p.m.