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16 lines
37 KiB
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{
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"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# GCAT version 5.00\n# Notes by Jason\n# 08/18/2011\n\n# Initialization\n\n\nPLATE.LETTERS = paste(rep(c(\"\", LETTERS), each = 26), rep(LETTERS, 26), sep=\"\")\nglobal.version.number = packageDescription(pkg=\"GCAT\")$Version \n\n########################################################################\n# #\n# Top-level functions for analysis of screening data from .csv files. #\n# #\n########################################################################\n# This functions is called directly by the user interface.\n# They in turn call the main function <gcat.fit.main> (below) multiple times for each data file provided in <file.list>. \n\n# Arguments:\n# file.list - a list of full paths to .csv files. all files must be in the same format (see <single.plate>)\n# single.plate - are the file in the single plate (wide) format vs. the multi-plate (long) format?\n# layout.file - (optional) provide full path to a layout file with strain and media definitions (applies to all files in list)\n\n# out.dir - name a directory to output the table of curve parameters to (defaults to working directory) \n# graphic.dir - name a directory to output the images of the fitted curves to (defaults to subdirectory \"pics\" of <out.dir> above)\n\n\n# add.constant- should be a numeric constant that will be added to each curve before the log transform (defaults to 1) \n# blank.value - user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n# start.index - which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n# growth.cutoff - minimum threshold for curve growth. \n# points.to.remove - a list of numbers referring to troublesome points that should be removed across all wells.\n# remove.jumps - should the slope checking function be on the lookout for large jumps in OD?\n \n# silent - should messages be returned to the console?\n# verbose - should sub-functions return messages to console? (when I say verbose, I mean it!)\n\n# Returns:\n# if <return.fit> = F (default), avector of full paths to all the files generated by the function.\n# otherwise, the fitted array of well objects. \n\n# Use this function to analyze any set of .csv files using the same plate layout info. \n\n#' Analyze screening growth data from the given .csv files.\n#' \n#' Top-level GCAT function \n#' \n#' @param file.list A list of full paths to .csv files. all files must be in the same format (see <single.plate>)\n#' @param single.plate The file in the single plate (wide) format vs. the multi-plate (long) format?\n#' @param layout.file Full path to a layout file with strain and media definitions (applies to all files in list)\n#' @param out.dir A directory to output the table of curve parameters to (defaults to working directory) \n#' @param graphic.dir A directory to output the images of the fitted curves to (defaults to subdirectory \"pics\" of <out.dir> above)\n#' @param use.linear.param Whether to use linear parameters or not
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