309 sc2 pc40

R/mc6_mthds.R

@@ -47,8 +47,7 @@
 #'   \item{noise}{Flag series as noisy if the quality of fit as calculated by the root mean square 
 #'   error (rmse) for the series is greater than the cutoff (coff); \eqn{rmse > coff}{rmse > coff}.}
 #'   \item{border}{Flag series if borderline activity is suspected based on modeled top parameter 
-#'   (top) relative to cutoff (coff); \eqn{|top|<=1.2*coff~or~|top|>=0.8*coff}{|top| <= 1.2(coff) or
-#'    |top| >= 0.8(coff)}.}
+#'   (top) relative to cutoff (coff); \eqn{0.8*coff<=|top|<=1.2*coff}.}
 #'   \item{overfit.hit}{Method not yet updated for tcpl implementation. Flag hit-calls that would 
 #'   get changed after doing the small N correction to the aic values.}
 #'   \item{efficacy.50}{Flag low efficacy hits if series has an active hit call (hitc >= 0.9) and 

R/sc2_mthds.R

@@ -65,6 +65,7 @@
 #'   \item{pc20}{Add a cutoff value of 20. Typically for percent of control data.}
 #'   \item{pc25}{Add a cutoff value of 25. Typically for percent of control data.}
 #'   \item{pc30}{Add a cutoff value of 30. Typically for percent of control data.}
+#'   \item{pc40}{Add a cutoff value of 40. Typically for percent of control data.}
 #'  }
 #' }
 #' 
@@ -251,6 +252,13 @@ sc2_mthds <- function() {
       e1 <- bquote(coff <- c(coff, 16))
       list(e1)
 
+    },
+
+    pc40 = function() {
+
+      e1 <- bquote(coff <- c(coff, 40))
+      list(e1)
+
     }
   )
 }

vignettes/Introduction_Appendices.Rmd

@@ -2212,8 +2212,7 @@ FlagDescription <- c("Flag series if model directionality is questionable, i.e.
                      square error $(rmse)$ for the series is greater than the cutoff $(coff)$; 
                      $rmse > coff$",
                      "Flag series if borderline activity is suspected based on modeled top 
-                     parameter $(top)$ relative to cutoff $(coff)$; $|top| <= 1.2 * coff$ or 
-                     $|top|>= 0.8 * coff$.",
+                     parameter $(top)$ relative to cutoff $(coff)$; $0.8 * coff <= |top| <= 1.2 * coff$",
                      "Flag series if the average number of replicates per concentration is less than
                      2; $nrep < 2$.",
                      "Flag series if 4 concentrations or less were tested; $nconc <= 4$.",