Changes between Version 1 and Version 2 of

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

Added information about the plug-in.



    v1 v2  
    11= CGH Data Dumper =
    3 A plug-in that dumps bioassay set data in several format. More info to come ...
     3The CGH Data Dumper plug-in exports typical BAC data in several
     4different simple formats readily accessible for e.g. Excel,
     5CGHExplorer, and MeV CGH viewer. The plug-in works on a normal
     6BASEfile (matrix mode). Therefore, before running this plug-in, you
     7might want to join array designs using the
     8[source:plugins/base1/ VirtualArray plug-in].
    5 === License ===
     10This plug-in is currently unsupported at supplied as is. The plug-in
     11is written by Johan Staaf at the Dept. of Oncology at Lund University.
    7 This plug-in is released under the [ GNU General Public License].
    9 === Download tQN ===
     14== Exported fields are ==
     16!ReporterId = BAC clone Id
     18!GeneSymbol = Gene symbols of genes mapped to the BAC clone. Could be bundled using:
     20 Chromosome
     22 Cytoband
     24!StartPosition = Start position in BP for the BAC clone
     26!EndPosition = End position in BP for the BAC clone
     28M = Log2(ratio)
     30Note that the CGH formats do require probes to be exported to have a
     31genomic mapping.
     34== Formats ==
     36=== Standard Format ===
     38Format of header line is the above common columns and then the assays
     39with assay names in the header.
     41=== Lite Format ===
     43Format of header line is reporterId, chromosome, start, stop, and then
     44the assays with assay names in the header. NOTE: This format is
     45compatible with MeV CGH viewer.
     47=== Sample Name export ===
     49Only the sample names are exported into a file. No spot data.
     51=== Sample Name and annotation export ===
     53The sample name and a chosen annotation is exported into a file. No
     54spot data.
     56=== Annotation statistics ===
     58By specifying in the appropiate text field below in the format
     59e.g. `|ER status|brca_family_status|..|` you can get a summary of how
     60many assays has a certain annotation value for each of the specified
     61annotation types.
     63=== BED format ===
     65This creates a format similar to BED format as defined by UCSC and
     66Ensembl. Contains four columns; chr, start, stop, amd reporterId. You
     67can use BED files to create your own tracks in the UCSC genome
     70=== Single file Lite ===
     72This creates one file for each assays. The file name speciefed as a
     73parameter will be the suffix to the assay name. E.g specifying
     74myfile.txt will create a file for Ca13928 as Ca13928_myfile.txt .The
     75format of the individual files are the Lite format (see above).
     77=== Complete annotations to file ===
     79The annotations for all assays are printed to a file. Blanks are
     80filled with NA
     82=== Selected annotations to file ===
     84Only selected annotations and their assays are printed to file. Blanks
     85are filled with NA.
     87=== Mev + annotations ===
     89An MeV compatible file is printed containing annotations. This format
     90is experimental and needs to be completed.
     92=== Annotation Display dump for selected annotations ===
     94For annotation display option. Enter selected annotations in the
     96{{{|ER Status|p_brca_family_status|etc..|}}}
     97These annotations will be separated and a matrix created with N rows =
     98N samples and for each annotation value type, a column will be made
     99with N rows, where each row entry is 1 (annotation value exists for
     100this assay) or 0, no annotation value.
     102== Parameters ==
     104 1. [Optional] Give a valid full file name for the created file.
     106 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.
     108 3. Select export mode. Either standard or standard_lite as described above, or format suitable for Agilent CGH-analytics software.
     110 4. Select annotation for sample name and annotation export
     112 5. Define annotation types for annotation statistics in the form `|ERstatus|brca_family_status|...|`
     115== Download and installation ==
     117There is currently no detailed notes on how to install the plug-in in
     118BASE 1, please fall back on the BASE 1 documentation on how to install
     121=== BASE 2 ===
     123In BASE 2 this plug-in can be run using the
     124Base1PluginExecuter. Simply create a configuration for the CGH Data
     125Dumper following these steps:
     127 1. To be written.
     130== License ==
     132This plug-in is released under the
     133[ GNU General Public License].