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83 lines
3.4 KiB
83 lines
3.4 KiB
% Generated by roxygen2 (4.1.1): do not edit by hand
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% Please edit documentation in R/GCAT.main.R
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\name{gcat.analysis.main}
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\alias{gcat.analysis.main}
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\title{Analyze screening growth data from the given .csv files.}
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\usage{
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gcat.analysis.main(file.list, single.plate, layout.file = NULL,
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out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""),
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add.constant = 0, blank.value = NULL, start.index = 2,
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growth.cutoff = 0.05, use.linear.param = F, use.loess = F,
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smooth.param = 0.1, lagRange = NA, totalRange = NA, specRange = NA,
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points.to.remove = 0, remove.jumps = F, time.input = NA,
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plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
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multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
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single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
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"Media Definition"), silent = T, verbose = F, return.fit = F,
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overview.jpgs = T)
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}
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\arguments{
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\item{file.list}{A list of full paths to .csv files. all files must be in the same format (see <single.plate>)}
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\item{single.plate}{The file in the single plate (wide) format vs. the multi-plate (long) format?}
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\item{layout.file}{Full path to a layout file with strain and media definitions (applies to all files in list)}
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\item{out.dir}{A directory to output the table of curve parameters to (defaults to working directory)}
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\item{graphic.dir}{A directory to output the images of the fitted curves to (defaults to subdirectory "pics" of <out.dir> above)}
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\item{add.constant}{A numeric constant that will be added to each curve before the log transform (defaults to 1)}
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\item{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.}
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\item{start.index}{Which timepoint should be used as the first one after inoculation (defaults to the 2th one)}
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\item{growth.cutoff}{Minimum threshold for curve growth.}
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\item{use.linear.param}{Whether to use linear parameters or not?}
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\item{use.loess}{Whether to use LOESS model or not?}
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\item{smooth.param}{Smoothing parameter for LOESS model.}
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\item{lagRange}{The heatmap specific range for lag time.}
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\item{totalRange}{The heatmap specific range for the achieved growth.}
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\item{specRange}{The heatmap specific range for spec growth rate.}
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\item{points.to.remove}{A list of numbers referring to troublesome points that should be removed across all wells.}
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\item{remove.jumps}{Should the slope checking function be on the lookout for large jumps in OD?}
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\item{time.input}{The time setting in which the current system is running?}
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\item{plate.nrow}{The number of rows in a plate.}
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\item{plate.ncol}{The number of columns in a plate.}
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\item{input.skip.lines}{If specified, this number of lines shall be skipped from the top when reading the input file with read.csv}
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\item{multi.column.headers}{The headers of the result tabular data when analyzing multiple plates at once.}
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\item{single.column.headers}{The headers of the result tebaular data when analyzaing a single plate.}
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\item{layout.sheet.headers}{The headers of the layout file?}
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\item{silent}{Shoulde messages be returned to the console?}
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\item{verbose}{Should sub-functions return messages to console? (when I say verbose, I mean it!)}
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\item{return.fit}{Whether should a fit well object is returned or not.}
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\item{overview.jpgs}{Should GCAT enable an overview image?}
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}
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\value{
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Depending on return.fit setting, an array of fitted well objects or a list of output files
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}
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\description{
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Top-level GCAT function
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}
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