preprocess.chipdata: Description: Profiling preprocessing script

In microbiome/HITChipDB: HITChipDB

Description

Arguments:

Usage

preprocess.chipdata(
  dbuser,
  dbpwd,
  dbname,
  verbose = TRUE,
  host = NULL,
  port = NULL,
  use.precalculated.phylogeny = NULL,
  summarization.methods = c("frpa", "sum"),
  which.projects = NULL,
  all.samples = TRUE,
  save.dir = ".",
  use.default.parameters = FALSE
)

Arguments

dbuser	MySQL username
dbpwd	MySQL password
dbname	MySQL database name
verbose	monitor processing through intermediate messages
host	host; needed with FTP connections
port	port; needed with FTP connections
use.precalculated.phylogeny	use precalculated phylogeny?
summarization.methods	List summarization methods to be included in output. With HITChip frpa always used; with other chips rpa always used. Other options: "sum", "ave"
which.projects	Optionally specify the projects to extract. All samples from these projects will be included.
all.samples	Use all samples from the selected project by default? TRUE / FALSE
save.dir	Output data folder
use.default.parameters	use.default.parameters

Value

Preprocessed data and parameters

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation("microbiome")

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