run.profiling.script: Run profiling script

In microbiome/HITChipDB: HITChipDB

Description

Profiling main script

Usage

run.profiling.script(
  dbuser,
  dbpwd,
  dbname,
  verbose = TRUE,
  host = NULL,
  port = NULL,
  summarization.methods = c("frpa", "sum"),
  which.projects = NULL,
  probe.parameters = NULL,
  save.dir = NULL,
  use.default.parameters = FALSE
)

Arguments

dbuser	MySQL username
dbpwd	MySQL password
dbname	MySQL database name (HITChip: "Phyloarray"; MITChip: "Phyloarray_MIT"; PITChip old: "Phyloarray_PIT"; PITChip new: "pitchipdb")
verbose	verbose
host	host; needed with FTP connections
port	port; needed with FTP connections
summarization.methods	List summarization methods to be included in output. For HITChip frpa always used; for 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.
probe.parameters	probe.parameters
save.dir	Output data folder
use.default.parameters	use.default.parameters

Value

Profiling parameters. Also writes output to the user-specified directory.

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation("microbiome")

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