import_hitchip: Import HITChip data

In microbiome/HITChipDB: HITChipDB

Description

Import HITChip output into phyloseq format.

Usage

import_hitchip(
  data.dir,
  method = "frpa",
  detection.threshold = 0,
  verbose = F,
  taxonomy = NULL,
  taxonomy.full = NULL
)

Arguments

data.dir	Profiling script output directory for reading the data.
method	Probe summarization method ("rpa" or "sum")
detection.threshold	Taxon absence/presence thresholds (typically 10^1.8 for HITChip)
verbose	verbose

Value

data matrix (phylo x samples)

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation('microbiome')

Examples

 ## Not run: 
  data.dir <- system.file("extdata", package = "microbiome")
  dat <- import_hitchip(data.dir)

## End(Not run)

microbiome/HITChipDB documentation built on June 7, 2020, 8:25 a.m.