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52 lines
2.1 KiB
52 lines
2.1 KiB
10 years ago
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{gcat.output.main}
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\alias{gcat.output.main}
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\title{Output function for generating files from fitted data.}
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\usage{
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gcat.output.main(fitted.well.array, out.prefix = "", source.file.list,
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upload.timestamp = NULL, add.constant, blank.value, start.index,
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growth.cutoff, points.to.remove, remove.jumps, out.dir = getwd(),
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graphic.dir = paste(out.dir, "/pics", sep = ""), overview.jpgs = T,
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use.linear.param = F, use.loess = F, plate.nrow = 8, plate.ncol = 12,
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unlog = F, silent = T)
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}
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\arguments{
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\item{fitted.well.array}{A list of fitted well objects.}
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\item{out.prefix}{Prefix that is in the name of output files.}
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\item{blank.value}{User can enter a blank OD measurement for uninoculated wells.
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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{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{out.dir}{name a directory to output the table of curve parameters to (defaults to working directory)}
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\item{graphic.dir}{name a directory to output the images of the fitted curves to
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(defaults to subdirectory "pics" of <out.dir> above)}
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\item{overview.jpgs}{should jpgs be generated for each plate with the overview graphic?
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This is for backwards compatibility with the old web server.}
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\item{unlog}{should exported graphics be transformed back to the OD scale?}
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\item{silent}{should messages be returned to the console?}
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\item{constant.added}{(should be the same value as add.constant above) -
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used to readjust for the constant added during the log transform when plotting ODs.}
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}
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\value{
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A list of output files if success.
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}
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\description{
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Handles files and directories, calls \code{table.out}, \code{plate.overview} and \code{view.fit}
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to generate output tables and graphics.
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}
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