summarize_probedata: Summarize probedata

In microbiome/HITChipDB: HITChipDB

Description

Summarize phylogenetic microarray probe-level data from given input folder.

Usage

summarize_probedata(
  data.dir = NULL,
  probedata = NULL,
  taxonomy = NULL,
  level,
  method,
  probe.parameters = NULL
)

Arguments

data.dir	Data folder.
probedata	probe-level data matrix in absolute domain
taxonomy	probe taxonomy
level	Summarization level
method	Summarization method
probe.parameters	Precalculater probe parameters. Optional.

Value

data matrix (taxa x samples)

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation('microbiome')

Examples

## Not run: 
#library(microbiome)
#data.directory <- system.file("extdata", package = "microbiome")
# Read oligo-level data (here: simulated example data)
#probedata <- read_hitchip(data.directory, method = "frpa")$probedata
# Read phylogeny map
# NOTE: use phylogeny.filtered for species/L1/L2 summarization
# Load taxonomy from output directory
#taxonomy <- GetPhylogeny("HITChip", "filtered")
# Summarize oligos into higher level phylotypes
#dat <- summarize_probedata(
#                 probedata = probedata,
#		 taxonomy = taxonomy, 
#                method = "rpa",
#		 level = "species")
#
## End(Not run)

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