GCAT5.0 released

2015-04-10 15:12:45 -05:00
commit 67544a10e6
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+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{transform.ODs}
+\alias{transform.ODs}
+\title{Transform.Ods}
+\usage{
+\method{transform}{ODs}(input.well, use.log = T, blank.value = NULL,
+  start.index = 2, negative.OD.cutoff = 10, constant.added = 1, ...)
+}
+\arguments{
+\item{input.well}{an object of class well}
+
+\item{use.log}{gets added to the "use.log" slot of the well object. this will determine whether the log-transformed data
+or raw normalized data is returned using the function \code{data.from}.}
+
+\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{start.index}{which timepoint should be used as the first one after inoculation (defaults to the 2th one)}
+
+\item{negative.OD.cutoff}{if any ODs below the specified blank value are detected before this index timepoint, the entire well is discarded.}
+}
+\description{
+This function adds a "log.OD" column to the "screen.data" slot of a well object with log-transformed data.
+The raw data is kept intact.
+It also checks to see if any of the raw OD values (before a certain timepoint) is below the blank OD.
+This can be disastrous for the log(OD) transform.
+}
+