BASEfile
section	plugin
uniqueName	onk.lu.se/enell/Smooth
versionNumber	151
name	Transformation: Smooth
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.
execName	run
geneAverages	0
serialFormat	1
url	http://baseplugins.thep.lu.se/
minChannels	2
maxChannels	0
leaveStdin	0
leaveStdout	0
estimatedTime	3600
defaultMaxRam	134217728
usedColumns	position\treporter\tchromosome\tstartPosition\tendPosition
usedFields	intensity1\tintensity2
columns	position	valueType	name	commonName	options	defaultValue	enumOptions	removed
%
1	h	section		30	smooth settings		0
2	i	w_size	Window size	30	3		0
3	e	w_type	Window size type	30	cl	bp\tBasePairs\tcl\tClones	0
4	e	average	Average metod	30	mean	mean\tMean\tmedian\tMedian	0
5	f	w	Weight	30	1.0		0