source: trunk/se/lu/onk/Smooth/doc/smooth.base @ 179

Last change on this file since 179 was 179, checked in by Johan Enell, 15 years ago
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2section plugin
4versionNumber 151
5name  Transformation: Smooth
6descr 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.
7execName  run
8geneAverages  0
9serialFormat  1
11minChannels 2
12maxChannels 0
13leaveStdin  0
14leaveStdout 0
15estimatedTime 3600
16defaultMaxRam 134217728
17usedColumns position\treporter\tchromosome\tstartPosition\tendPosition
18usedFields  intensity1\tintensity2
19columns position  valueType name  commonName  options defaultValue  enumOptions removed
211 h section   30  smooth settings   0
222 i w_size  Window size 30  3   0
233 e w_type  Window size type  30  cl  bp\tBasePairs\tcl\tClones 0
244 e average Average metod 30  mean  mean\tMean\tmedian\tMedian  0
255 f w Weight  30  1.0   0
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