diff --git a/R/getFittedValues.R b/R/getFittedValues.R index 5fa78ee..1a3a1af 100644 --- a/R/getFittedValues.R +++ b/R/getFittedValues.R @@ -14,6 +14,7 @@ #' @param size.factor.offset (Optional) An offset to be used to rescale the fitted values. Can be generated easily with \code{\link{createCellOffset}}. No need to provide if the GEE backend was used. Defaults to NULL. #' @param log1p.norm (Optional) Should log1p-normalized versions of expression & model predictions be returned as well? Defaults to TRUE. #' @param cell.meta.data (Optional) A data.frame of metadata values for each cell (celltype label, subject characteristics, tissue type, etc.) that will be included in the result table. Defaults to NULL. +#' @param is.gee Was the GEE mode used to fit the models? Defaults to FALSE. #' @param id.vec (Optional) A vector of subject IDs used in fitting GEE or GLMM models. Defaults to NULL. #' @param ci.alpha (Optional) The pre-specified Type I Error rate used in generating (\eqn{1 - \alpha})\% CIs. Defaults to good old 0.05. #' @param filter.lineage (Optional) A character vector of lineages to filter out before generating the final plot. Should be letters, i.e. lineage "A" or "B". Defaults to NULL. @@ -35,6 +36,7 @@ getFittedValues <- function(test.dyn.res = NULL, size.factor.offset = NULL, log1p.norm = TRUE, cell.meta.data = NULL, + is.gee = FALSE, id.vec = NULL, ci.alpha = 0.05, filter.lineage = NULL) { diff --git a/man/getFittedValues.Rd b/man/getFittedValues.Rd index f8234b9..0ddf96d 100644 --- a/man/getFittedValues.Rd +++ b/man/getFittedValues.Rd @@ -12,6 +12,7 @@ getFittedValues( size.factor.offset = NULL, log1p.norm = TRUE, cell.meta.data = NULL, + is.gee = FALSE, id.vec = NULL, ci.alpha = 0.05, filter.lineage = NULL @@ -32,6 +33,8 @@ getFittedValues( \item{cell.meta.data}{(Optional) A data.frame of metadata values for each cell (celltype label, subject characteristics, tissue type, etc.) that will be included in the result table. Defaults to NULL.} +\item{is.gee}{Was the GEE mode used to fit the models? Defaults to FALSE.} + \item{id.vec}{(Optional) A vector of subject IDs used in fitting GEE or GLMM models. Defaults to NULL.} \item{ci.alpha}{(Optional) The pre-specified Type I Error rate used in generating (\eqn{1 - \alpha})\% CIs. Defaults to good old 0.05.}