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enell |
BASEfile |
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enell |
section plugin |
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enell |
uniqueName onk.lu.se/enell/Smooth |
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enell |
versionNumber 151 |
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enell |
name Transformation: Smooth |
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enell |
descr Smooth can be used to reduce experimental noise over the chromosome profile. It uses a sliding window over the gene where the size of the window is either number of clones or basepairs. If basepairs is choosen a clone is said to be inside the window if more then half of the gene is inside. Each clone is fitted to the local median or mean in the window and the user can choose the impact by using a simple weight.\r\n\r\nParameters:\r\n\r\nWindow size - The _whole_ size of the window. Depending of the window type it is either number of basepairs or number of clones.\r\n\r\nWindow size type - If the window should be in basepairs or in number of clones.\r\n\r\nAverage metod - If mean or median should be used to calculate the fit. \r\n\r\nWeight - A number between 0 an 1 that determins how close each clone should be to the fit. 1 means that the clone is right on and 0 means that the clone wont move at all. |
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enell |
execName run |
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enell |
geneAverages 0 |
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enell |
serialFormat 1 |
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enell |
url http://baseplugins.thep.lu.se/ |
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enell |
minChannels 2 |
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enell |
maxChannels 0 |
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enell |
leaveStdin 0 |
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enell |
leaveStdout 0 |
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enell |
estimatedTime 3600 |
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enell |
defaultMaxRam 134217728 |
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enell |
usedColumns position\treporter\tchromosome\tstartPosition\tendPosition |
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enell |
usedFields intensity1\tintensity2 |
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enell |
columns position valueType name commonName options defaultValue enumOptions removed |
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enell |
20 |
% |
| 148 |
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enell |
1 h section 30 smooth settings 0 |
| 148 |
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enell |
2 i w_size Window size 30 3 0 |
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enell |
3 e w_type Window size type 30 cl bp\tBasePairs\tcl\tClones 0 |
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enell |
4 e average Average metod 30 mean mean\tMean\tmedian\tMedian 0 |
| 158 |
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enell |
5 f w Weight 30 1.0 0 |
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enell |
26 |
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