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Updated master to SVN trunk revision 572

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This commit is contained in:
Yury V Bukhman
2015-06-26 15:04:35 -05:00
parent 67544a10e6
commit 2d658405a1
184 changed files with 8236 additions and 6182 deletions
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R/GCAT/man/gcat.analysis.main.Rd
+19 -9
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@@ -1,18 +1,20 @@
% Generated by roxygen2 (4.0.2): do not edit by hand
% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/GCAT.main.R
\name{gcat.analysis.main}
\alias{gcat.analysis.main}
\title{Analyze screening growth data from the given .csv files.}
\usage{
gcat.analysis.main(file.list, single.plate, layout.file = NULL,
out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""),
add.constant = 0.1, blank.value = NULL, start.index = 2,
add.constant = 0, blank.value = NULL, start.index = 2,
growth.cutoff = 0.05, use.linear.param = F, use.loess = F,
smooth.param = 0.1, points.to.remove = 0, remove.jumps = F,
time.input = NA, plate.nrow = 8, plate.ncol = 12,
input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD",
"Time"), single.column.headers = c("", "A1"),
layout.sheet.headers = c("Strain", "Media Definition"), silent = T,
verbose = F, return.fit = F, overview.jpgs = T)
smooth.param = 0.1, lagRange = NA, totalRange = NA, specRange = NA,
points.to.remove = 0, remove.jumps = F, time.input = NA,
plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
"Media Definition"), silent = T, verbose = F, return.fit = F,
overview.jpgs = T)
}
\arguments{
\item{file.list}{A list of full paths to .csv files. all files must be in the same format (see <single.plate>)}
@@ -39,6 +41,12 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
\item{smooth.param}{Smoothing parameter for LOESS model.}
\item{lagRange}{The heatmap specific range for lag time.}
\item{totalRange}{The heatmap specific range for the achieved growth.}
\item{specRange}{The heatmap specific range for spec growth rate.}
\item{points.to.remove}{A list of numbers referring to troublesome points that should be removed across all wells.}
\item{remove.jumps}{Should the slope checking function be on the lookout for large jumps in OD?}
@@ -61,10 +69,12 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
\item{verbose}{Should sub-functions return messages to console? (when I say verbose, I mean it!)}
\item{return.fit}{Whether should a fit well object is returned or not.}
\item{overview.jpgs}{Should GCAT enable an overview image?}
}
\value{
A list of the output files.
Depending on return.fit setting, an array of fitted well objects or a list of output files
}
\description{
Top-level GCAT function