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Commiting branch GCAT_6.0 at SVN revision 572

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Yury V Bukhman
2015-06-26 15:51:35 -05:00
parent 2d658405a1
commit c7fb48ce68
14 changed files with 40 additions and 27 deletions
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R/GCAT/man/gcat.analysis.main.Rd
+9 -10
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@@ -6,15 +6,14 @@
\usage{
gcat.analysis.main(file.list, single.plate, layout.file = NULL,
out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""),
add.constant = 0, blank.value = NULL, start.index = 2,
growth.cutoff = 0.05, use.linear.param = F, use.loess = F,
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)
add.constant = 0, blank.value, start.index, growth.cutoff = 0.05,
use.linear.param = F, use.loess = F, 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>)}
@@ -29,7 +28,7 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
\item{add.constant}{A numeric constant that will be added to each curve before the log transform (defaults to 1)}
\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.}
\item{blank.value}{User can enter a blank OD measurement for uninoculated wells. if NULL, assumes the first OD measurement of each well to be blank.}
\item{start.index}{Which timepoint should be used as the first one after inoculation (defaults to the 2th one)}