Description Usage Arguments Value Author(s) References
Profiling main script
1 2 3 4 5 6 7 8 9 10 11 12 13 |
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 |
Profiling parameters. Also writes output to the user-specified directory.
Contact: Leo Lahti microbiome-admin@googlegroups.com
See citation("microbiome")
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