Changes between Version 1 and Version 2 of se.lu.onk.CGHDataDumper

Timestamp:

Jun 11, 2008, 11:53:21 PM (16 years ago)

Author:

Jari Häkkinen

Comment:

Added information about the plug-in.

se.lu.onk.CGHDataDumper

@@ -1 +1 @@
 = CGH Data Dumper =
 
-A plug-in that dumps bioassay set data in several format. More info to come ...
+The CGH Data Dumper plug-in exports typical BAC data in several
+different simple formats readily accessible for e.g. Excel,
+CGHExplorer, and MeV CGH viewer. The plug-in works on a normal
+BASEfile (matrix mode). Therefore, before running this plug-in, you
+might want to join array designs using the
+[source:plugins/base1/se.lu.onk/trunk/VirtualArray VirtualArray plug-in].
 
-=== License ===
+This plug-in is currently unsupported at supplied as is. The plug-in
+is written by Johan Staaf at the Dept. of Oncology at Lund University.
 
-This plug-in is released under the [http://www.gnu.org/copyleft/gpl.html GNU General Public License].
 
-=== Download tQN ===
+== Exported fields are ==
+
+!ReporterId = BAC clone Id
+
+!GeneSymbol = Gene symbols of genes mapped to the BAC clone. Could be bundled using:
+
+ Chromosome
+
+ Cytoband
+
+!StartPosition = Start position in BP for the BAC clone
+
+!EndPosition = End position in BP for the BAC clone
+
+M = Log2(ratio)
+
+Note that the CGH formats do require probes to be exported to have a
+genomic mapping.
+
+
+== Formats ==
+
+=== Standard Format ===
+
+Format of header line is the above common columns and then the assays
+with assay names in the header.
+
+=== Lite Format ===
+
+Format of header line is reporterId, chromosome, start, stop, and then
+the assays with assay names in the header. NOTE: This format is
+compatible with MeV CGH viewer.
+
+=== Sample Name export ===
+
+Only the sample names are exported into a file. No spot data.
+
+=== Sample Name and annotation export ===
+
+The sample name and a chosen annotation is exported into a file. No
+spot data.
+
+=== Annotation statistics ===
+
+By specifying in the appropiate text field below in the format
+e.g. `|ER status|brca_family_status|..|` you can get a summary of how
+many assays has a certain annotation value for each of the specified
+annotation types.
+
+=== BED format ===
+
+This creates a format similar to BED format as defined by UCSC and
+Ensembl. Contains four columns; chr, start, stop, amd reporterId. You
+can use BED files to create your own tracks in the UCSC genome
+browser.
+
+=== Single file Lite ===
+
+This creates one file for each assays. The file name speciefed as a
+parameter will be the suffix to the assay name. E.g specifying
+myfile.txt will create a file for Ca13928 as Ca13928_myfile.txt .The
+format of the individual files are the Lite format (see above).
+
+=== Complete annotations to file ===
+
+The annotations for all assays are printed to a file. Blanks are
+filled with NA
+
+=== Selected annotations to file ===
+
+Only selected annotations and their assays are printed to file. Blanks
+are filled with NA.
+
+=== Mev + annotations ===
+
+An MeV compatible file is printed containing annotations. This format
+is experimental and needs to be completed.
+
+=== Annotation Display dump for selected annotations ===
+
+For annotation display option. Enter selected annotations in the
+format:
+{{{|ER Status|p_brca_family_status|etc..|}}}
+These annotations will be separated and a matrix created with N rows =
+N samples and for each annotation value type, a column will be made
+with N rows, where each row entry is 1 (annotation value exists for
+this assay) or 0, no annotation value.
+
+== Parameters ==
+
+ 1. [Optional] Give a valid full file name for the created file.
+
+ 2. [Optional] Sort the data as well. NOTE! Using the sort option may require you to increase the RAM usage considerably if working with large data sets.
+
+ 3. Select export mode. Either standard or standard_lite as described above, or format suitable for Agilent CGH-analytics software.
+
+ 4. Select annotation for sample name and annotation export
+
+ 5. Define annotation types for annotation statistics in the form `|ERstatus|brca_family_status|...|`
+
+
+== Download and installation ==
+
+There is currently no detailed notes on how to install the plug-in in
+BASE 1, please fall back on the BASE 1 documentation on how to install
+plug-ins.
+
+=== BASE 2 ===
+
+In BASE 2 this plug-in can be run using the
+Base1PluginExecuter. Simply create a configuration for the CGH Data
+Dumper following these steps:
+
+ 1. To be written.
+
+
+== License ==
+
+This plug-in is released under the
+[http://www.gnu.org/copyleft/gpl.html GNU General Public License].