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


Ignore:
Timestamp:
Jun 11, 2008, 11:53:21 PM (13 years ago)
Author:
Jari Häkkinen
Comment:

Added information about the plug-in.

Legend:

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  • se.lu.onk.CGHDataDumper

    v1 v2  
    11= CGH Data Dumper =
    22
    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/se.lu.onk/trunk/VirtualArray VirtualArray plug-in].
    49
    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.
    612
    7 This plug-in is released under the [http://www.gnu.org/copyleft/gpl.html GNU General Public License].
    813
    9 === Download tQN ===
     14== Exported fields are ==
     15
     16!ReporterId = BAC clone Id
     17
     18!GeneSymbol = Gene symbols of genes mapped to the BAC clone. Could be bundled using:
     19
     20 Chromosome
     21
     22 Cytoband
     23
     24!StartPosition = Start position in BP for the BAC clone
     25
     26!EndPosition = End position in BP for the BAC clone
     27
     28M = Log2(ratio)
     29
     30Note that the CGH formats do require probes to be exported to have a
     31genomic mapping.
     32
     33
     34== Formats ==
     35
     36=== Standard Format ===
     37
     38Format of header line is the above common columns and then the assays
     39with assay names in the header.
     40
     41=== Lite Format ===
     42
     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.
     46
     47=== Sample Name export ===
     48
     49Only the sample names are exported into a file. No spot data.
     50
     51=== Sample Name and annotation export ===
     52
     53The sample name and a chosen annotation is exported into a file. No
     54spot data.
     55
     56=== Annotation statistics ===
     57
     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.
     62
     63=== BED format ===
     64
     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
     68browser.
     69
     70=== Single file Lite ===
     71
     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).
     76
     77=== Complete annotations to file ===
     78
     79The annotations for all assays are printed to a file. Blanks are
     80filled with NA
     81
     82=== Selected annotations to file ===
     83
     84Only selected annotations and their assays are printed to file. Blanks
     85are filled with NA.
     86
     87=== Mev + annotations ===
     88
     89An MeV compatible file is printed containing annotations. This format
     90is experimental and needs to be completed.
     91
     92=== Annotation Display dump for selected annotations ===
     93
     94For annotation display option. Enter selected annotations in the
     95format:
     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.
     101
     102== Parameters ==
     103
     104 1. [Optional] Give a valid full file name for the created file.
     105
     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.
     107
     108 3. Select export mode. Either standard or standard_lite as described above, or format suitable for Agilent CGH-analytics software.
     109
     110 4. Select annotation for sample name and annotation export
     111
     112 5. Define annotation types for annotation statistics in the form `|ERstatus|brca_family_status|...|`
     113
     114
     115== Download and installation ==
     116
     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
     119plug-ins.
     120
     121=== BASE 2 ===
     122
     123In BASE 2 this plug-in can be run using the
     124Base1PluginExecuter. Simply create a configuration for the CGH Data
     125Dumper following these steps:
     126
     127 1. To be written.
     128
     129
     130== License ==
     131
     132This plug-in is released under the
     133[http://www.gnu.org/copyleft/gpl.html GNU General Public License].