run.profiling.script: Run profiling script

Description Usage Arguments Value Author(s) References

Description

Profiling main script

Usage

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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 microbiome-admin@googlegroups.com

References

See citation("microbiome")


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