diff --git a/R/select_transcripts.R b/R/select_transcripts.R index bd3eb8f..a7277fd 100644 --- a/R/select_transcripts.R +++ b/R/select_transcripts.R @@ -3,11 +3,19 @@ #' Helper function to select which experimental model will be used to generate the qSVs. #' #' @param type A `character(1)` specifying the transcripts set type. -#' These were determined by Joshua M. Stolz et al, 2022. Here the names "cell_component", "top1500", and "standard" refer to models that were determined to be effective in removing degradation effects. -#' The "standard" model involves taking the union of the top 1000 transcripts associated with degradation from the interaction model and the main effect model. -#' The "top1500" model is the same as the "standard model except the union of the top 1500 genes associated with degradation is selected. -#' The most effective of our models, "cell_component", involved deconvolution of the degradation matrix to determine the proportion of cell types within our studied tissue. -#' These proportions were then added to our `model.matrix()` and the union of the top 1000 transcripts in the interaction model, the main effect model, and the cell proportions model were used to generate this model of qSVs. +#' These were determined by Joshua M. Stolz +#' et al, 2022. Here the names "cell_component", "top1500", and "standard" refer +#' to models that were determined to be effective in removing degradation +#' effects. The "standard" model involves taking the union of the top 1000 +#' transcripts associated with degradation from the interaction model and the +#' main effect model. The "top1500" model is the same as the "standard" model +#' except the union of the top 1500 genes associated with degradation is +#' selected. The most effective of our models, "cell_component", involved +#' deconvolution of the degradation matrix to determine the proportion of cell +#' types within our studied tissue. These proportions were then added to our +#' `model.matrix()` and the union of the top 1000 transcripts in the interaction +#' model, the main effect model, and the cell proportions models (main and +#' interaction) were used to generate this model of qSVs. #' #' @return A `character()` with the transcript IDs. #' @export diff --git a/man/DEqual.Rd b/man/DEqual.Rd index a47fbd1..5214bee 100644 --- a/man/DEqual.Rd +++ b/man/DEqual.Rd @@ -19,7 +19,7 @@ DEqual( from Differential Expression, typically generated with \code{limma::topTable()}. \code{rownames(DE)} must have transcript Ensembl/Gencode IDs.} -\item{deg_tstats}{an optional\code{data.frame()} with a column "t" containing +\item{deg_tstats}{an optional \code{data.frame()} with a column "t" containing t-statistics resulted from a degradation experiment. Default is the internal \code{qsvaR::degradation_tstats} from the package authors.} diff --git a/man/select_transcripts.Rd b/man/select_transcripts.Rd index cbbe671..1614fcb 100644 --- a/man/select_transcripts.Rd +++ b/man/select_transcripts.Rd @@ -8,11 +8,19 @@ select_transcripts(type = c("cell_component", "top1500", "standard")) } \arguments{ \item{type}{A \code{character(1)} specifying the transcripts set type. -These were determined by Joshua M. Stolz et al, 2022. Here the names "cell_component", "top1500", and "standard" refer to models that were determined to be effective in removing degradation effects. -The "standard" model involves taking the union of the top 1000 transcripts associated with degradation from the interaction model and the main effect model. -The "top1500" model is the same as the "standard model except the union of the top 1500 genes associated with degradation is selected. -The most effective of our models, "cell_component", involved deconvolution of the degradation matrix to determine the proportion of cell types within our studied tissue. -These proportions were then added to our \code{model.matrix()} and the union of the top 1000 transcripts in the interaction model, the main effect model, and the cell proportions model were used to generate this model of qSVs.} +These were determined by Joshua M. Stolz +et al, 2022. Here the names "cell_component", "top1500", and "standard" refer +to models that were determined to be effective in removing degradation +effects. The "standard" model involves taking the union of the top 1000 +transcripts associated with degradation from the interaction model and the +main effect model. The "top1500" model is the same as the "standard" model +except the union of the top 1500 genes associated with degradation is +selected. The most effective of our models, "cell_component", involved +deconvolution of the degradation matrix to determine the proportion of cell +types within our studied tissue. These proportions were then added to our +\code{model.matrix()} and the union of the top 1000 transcripts in the interaction +model, the main effect model, and the cell proportions models (main and +interaction) were used to generate this model of qSVs.} } \value{ A \code{character()} with the transcript IDs. diff --git a/man/transcripts.Rd b/man/transcripts.Rd index 1721a58..4b560fc 100644 --- a/man/transcripts.Rd +++ b/man/transcripts.Rd @@ -12,12 +12,20 @@ Each string is a GENCODE transcript IDs. transcripts } \description{ -An object storing three lists of transcripts each corresponding to a model used in the degradation experiment. -These were determined by Joshua M. Stolz et al, 2022. Here the names "cell_component", "top1500", and "standard" refer to models that were determined to be effective in removing degradation effects. -The "standard" model involves taking the union of the top 1000 transcripts associated with degradation from the interaction model and the main effect model. -The "top1500" model is the same as the "standard" model except the union of the top 1500 genes associated with degradation is selected. -The most effective of our models, "cell_component", involved deconvolution of the degradation matrix to determine the proportion of cell types within our studied tissue. -These proportions were then added to our \code{model.matrix()} and the union of the top 1000 transcripts in the interaction model, the main effect model, and the cell proportions model were used to generate this model of qSVs. +An object storing three lists of transcripts each corresponding to a model +used in the degradation experiment. These were determined by Joshua M. Stolz +et al, 2022. Here the names "cell_component", "top1500", and "standard" refer +to models that were determined to be effective in removing degradation +effects. The "standard" model involves taking the union of the top 1000 +transcripts associated with degradation from the interaction model and the +main effect model. The "top1500" model is the same as the "standard" model +except the union of the top 1500 genes associated with degradation is +selected. The most effective of our models, "cell_component", involved +deconvolution of the degradation matrix to determine the proportion of cell +types within our studied tissue. These proportions were then added to our +\code{model.matrix()} and the union of the top 1000 transcripts in the interaction +model, the main effect model, and the cell proportions models (main and +interaction) were used to generate this model of qSVs. } \seealso{ \link{select_transcripts}