read_hitchip: Read HITChip

In microbiome/HITChipDB: HITChipDB

Description

Read HITChip output and preprocess into phyloseq format.

Usage

read_hitchip(
  data.dir,
  method = "rpa",
  detection.threshold = 0,
  verbose = F,
  taxonomy = NULL
)

Arguments

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

Details

Converts the probe-level data matrix and probe-level taxonomy table to phylotype-level HITChip data. Returns the probe-level data (data matrix and taxonomies) and the phylotype-level phyloseq object. There are two versions of probe-level taxonomy. The full version includes all probes in the probe-level data. The filtered version includes those probes that have been used to aggregate probes into phylotype level.

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 <- read_hitchip(data.dir)

## End(Not run)

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