16 lines
17 KiB
Plaintext
16 lines
17 KiB
Plaintext
|
{
|
||
|
|
"contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see <http://www.gnu.org/licenses/>.\n\n########################################################################\n# #\n# <well> class definition and functions. Objects contain raw #\n# data from screening runs on single wells from 96-well plates, and #\n# other slots for processing and model-fitting details. #\n# #\n########################################################################\n\n# Windows OS compatibility\nSys.setlocale(locale=\"C\")\n#require(RExcelXML)\n\n# Treat nls and loess as S4 classes to avoid warnings\nsetOldClass(\"nls\")\nsetOldClass(\"loess\")\nsetClass(\"well\", representation(position = \"character\",\n\t\t\t\t\t well.info = \"list\",\n\t\t\t\t\t screen.data = \"data.frame\", \n start.index = \"numeric\",\n\t\t\t\t\t use.log = \"logical\",\n\t\t\t\t\t norm = \"numeric\",\n\t\t\t\t\t curve.par = \"list\", \n\t\t\t\t\t fit.par = \"list\",\n fit.std.err = \"list\",\n\t\t\t\t\t equation = \"expression\",\n\t\t\t\t\t model.name = \"character\",\n\t\t\t\t\t fit.info = \"character\",\n\t\t\t\t\t add.info = \"character\",\n inflection.time = \"numeric\",\n rss = \"numeric\",\n loess = \"loess\",\n nls = \"nls\"))\n\n# Slots:\n# position - 3-member vector containing identifying information for the well: row (letters), column (numbers) and plate ID. \n# well.info - a list containing strain and media names if provided\n# screen.data - a data frame with Time and raw OD values. This is the only slot that is filled upon creation of a well object. \n# as different functions are run on the well the data frame gets filled with additional columns. \n# use.log - a single logical value denoting whether to return log-transformed values when data is requested from the well\n# norm - a value to subtract from all OD values before returning data. filled by <normalize.ODs> (see normalize.and.transform.R)\n# curve.par - a list of parameters that denote whether the well is empty, whether it contains ODs indicating a viable culture, whether it tanks at a certain timepoint. \n\n# if model fitting using <fit.model> is successful:\n# fit.par - will be a list containing the fitted model parameters\n# fit.std.err - will be a list containing the standard errors for the fitted model parameters\n# equation - will contain an expression for evaluating the successfully fitted model \n# model.name - will contain the name of the successfully fit model\n\n# fit.info - a message with info about whether the fit was successful, failed, or skipped. \n# add.info - a message with info about whether jumps in OD were detected or removed, or if ODs were detected below the blank OD.\n# inflection.time - the Time value at the point where the specific growth is located. no longer a formula param NWD\n# rss - residual sum of squares\n# loess - object returned by running loess on the normalized well data\n# nls - object returned by running nls on the normalized well data\n\nsetGeneric(\"getPositio
|
||
|
|
"created" : 1425413290697.000,
|
||
|
|
"dirty" : false,
|
||
|
|
"encoding" : "UTF-8",
|
||
|
|
"folds" : "",
|
||
|
|
"hash" : "2437520955",
|
||
|
|
"id" : "4DC8D1",
|
||
|
|
"lastKnownWriteTime" : 1425509121,
|
||
|
|
"path" : "~/Documents/GCAT4/trunk/R/GCAT/R/class.well.R",
|
||
|
|
"project_path" : "R/class.well.R",
|
||
|
|
"properties" : {
|
||
|
|
},
|
||
|
|
"source_on_save" : false,
|
||
|
|
"type" : "r_source"
|
||
|
|
}
|