@@ -19,6 +19,7 @@ COMPASS(

   verbose = TRUE,

   dropDegreeOne = FALSE,

   init_with_fisher = FALSE,

+  run_model_or_return_data = "run_model",

   ...

 )

 }

@@ -71,6 +72,8 @@ and merge them with the negative subset.}

 \item{init_with_fisher}{Boolean;initialize from fisher's exact test. Any subset and subject with lower 95% log odds estimate >1 will be initialized as a responder.

 Otherwise initialize very subject and subset as a responder except those where ps <= pu.}

+\item{run_model_or_return_data}{\code{character} defaults to \code{"run_model"} otherwise set it to \code{"return_data"} in order to not fit the model just return the data set needed for modeling. Useful for extracting the boolean counts.}

+

 \item{...}{Other arguments; currently unused.}

 }

 \value{

@@ -29,13 +29,11 @@ from a \code{COMPASS} fit object.

 The posterior items retrieved are described as follows::

 \describe{

-\item{\code{PosteriorPs}:}{The posterior probability that the samples

-subjected to the 'treatment', or 'stimulated', condition responded.}

-\item{\code{PosteriorPu:}}{The posterior probability that the samples

-subjected to the 'control', or 'unstimulated', condition responded.}

-\item{\code{PosteriorDiff}:}{The difference in posterior response rates,

+\item{\code{PosteriorPs}:}{The posterior estimate of the proportion of cells in the stimulated sample.}

+\item{\code{PosteriorPu:}}{The posterior estimate of the proportio of cells in the unstimulated sample.}

+\item{\code{PosteriorDiff}:}{The difference in posterior proportions,

 as described above.}

-\item{\code{PosteriorLogDiff}:}{The difference in the log response rates,

+\item{\code{PosteriorLogDiff}:}{The difference in the log posterior proportions,

 as described above.}

 }

 }