From ce06c9d38a431757f2b0d95a97d48fb28ca8effb Mon Sep 17 00:00:00 2001 From: Feshuk Date: Mon, 2 Dec 2024 13:07:15 -0500 Subject: [PATCH 1/3] add pc40 mthd --- R/sc2_mthds.R | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/R/sc2_mthds.R b/R/sc2_mthds.R index 9b251255..282c5c51 100644 --- a/R/sc2_mthds.R +++ b/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) + } ) } From 848c62372f1405200eb467b682eee2c506141e8c Mon Sep 17 00:00:00 2001 From: Feshuk Date: Mon, 2 Dec 2024 13:26:39 -0500 Subject: [PATCH 2/3] fix borderline flag typos at mc6 --- R/mc6_mthds.R | 3 +-- vignettes/Introduction_Appendices.Rmd | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/R/mc6_mthds.R b/R/mc6_mthds.R index eb997c17..17088d1a 100644 --- a/R/mc6_mthds.R +++ b/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 diff --git a/vignettes/Introduction_Appendices.Rmd b/vignettes/Introduction_Appendices.Rmd index 4a6a0a1c..66a6c04c 100644 --- a/vignettes/Introduction_Appendices.Rmd +++ b/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; $nconc <= 4$.", From 47027e29b8fc9a7fdc26302eea6fce2ba0fdfc6d Mon Sep 17 00:00:00 2001 From: Feshuk Date: Mon, 2 Dec 2024 17:13:55 -0500 Subject: [PATCH 3/3] regen documentation --- man/MC6_Methods.Rd | 3 +-- man/SC2_Methods.Rd | 1 + 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/man/MC6_Methods.Rd b/man/MC6_Methods.Rd index 39718d3c..8cf0c072 100644 --- a/man/MC6_Methods.Rd +++ b/man/MC6_Methods.Rd @@ -51,8 +51,7 @@ available in the package vignette, "Data_processing." \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 diff --git a/man/SC2_Methods.Rd b/man/SC2_Methods.Rd index b71536bf..201bb80a 100644 --- a/man/SC2_Methods.Rd +++ b/man/SC2_Methods.Rd @@ -69,6 +69,7 @@ vignette, "Data_processing." \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.} } }