This function facilitates setting options for the acmap titer merging process by returning a list of option settings.
RacMerge.options(sd_limit = NULL, dilution_stepsize = 1, method = NULL)When merging titers, titers that have a standard deviation of this amount or greater on the log2 scale will be set to "*" and excluded. Setting this to NA removes any limit. The default value will be NA, unless the titer merge method is specified as "lispmds" in which case the default is 1 and standard deviation is calculated by division by n, instead of n-1, in order to maintain backwards compatibility with previous approaches.
The dilution stepsize to assume when merging titers (see
dilutionStepsize())
The titer merging method to use, either a string of "conservative" or "likelihood", or a user defined function. See details.
Returns a named list of merging options
When merging measured titers, the general approach is to take the geometric mean and use that as the merged titer, however in particular when < values are present there are different options that can be employed. In older versions of Racmacs, < values were converted to maximum possible numeric titer after accounting for the dilution_stepsize factor, then the geometric mean was taken. This approach can be used by specifying the method as "likelihood" since, this approach gives a very rough approximation of the most likely mean numeric value. In contrast, the "conservative" method and current default returns the highest < value that satisfies all the values that were measured. As an example merging <10 and 20, (assuming dilution_stepsize = 1) would return a value of 10 with the "likelihood" method and <40 with the "conservative" method.
Other map merging functions:
htmlMergeReport(),
mergeMaps(),
mergeReport(),
splitTiterLayers()