summarize_probedata {RPA} | R Documentation |
Summarize phylogenetic microarray probe-level data from given input folder.
summarize_probedata( data.dir = NULL, probedata = NULL, taxonomy = NULL, level, method, probe.parameters = NULL )
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. |
data matrix (taxa x samples)
Contact: Leo Lahti microbiome-admin@googlegroups.com
See citation('microbiome')
## 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)