removed confusing references to covComb_tx_deg when used as example RSE

R/degradation_tstats-data.R

@@ -1,10 +1,10 @@
 #' Degradation time t-statistics
 #'
-#' These t-statistics are derived from the same data that was used for
-#' [rse_tx]. They are the results from main model where we determined
-#' the relationship with degradation time adjusting for the brain region (so
-#' parallel degradation effects across brain regions). They are used for
-#' plotting in `DEqual()`.
+#' These t-statistics are derived from the degradation timepoints data
+#' built into qsvaR. They are the results from multiple models where
+#' we determined the association of transcripts with degradation time
+#' adjusting for brain region (so parallel degradation effects across
+#' brain regions). They are used for plotting in `DEqual()`.
 #'
 #' @name degradation_tstats
 #' @docType data

R/qSVA.R

@@ -3,14 +3,14 @@
 #' @param rse_tx A [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class] object containing
 #' the transcript data desired to be studied.
 #' @param type a character string specifying which model you would
-#'  like to use when selecting a degradation matrix.
-#' @param sig_transcripts A list of transcripts that are associated with
-#' degradation signal. Use `select_transcripts()` to select sets of transcripts
-#' identified by the qSVA expanded paper. Specifying a `character()` input of
-#' ENSEMBL transcript IDs (or whatever values you have at `rownames(rse_tx)`)
-#' obtained outside of `select_transcripts()` overrides
-#' the user friendly `type` argument. That is, this argument provides more fine
-#' tuning options for advanced users.
+#'  like to use from the sets of signature transcripts identified
+#'  by the qsvaR package. This can be omitted if a custom set of
+#'  transcripts is provided to sig_transcripts.
+#' @param sig_transcripts A list of transcript IDs that are associated
+#'  with degradation signal. Specifying a `character()` input with ENSEMBL
+#' transcript IDs (whose values should match entries in `rownames(rse_tx)`).
+#' This argument provides a custom list of transcripts for adjusting
+#' for degradation; this should be used instead of the `type` argument.
 #' @param mod Model Matrix with necessary variables the you would
 #'  model for in differential expression
 #' @param assayname character string specifying the name of

R/rse_tx-data.R

@@ -0,0 +1,13 @@
+#' Example of RSE object with RNA-seq transcript quantification data
+#'
+#' This data is a [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class]
+#' with transcript quantification data stored in an "tpm" assay. It is
+#'  used to demonstrate the use of qsvaR in bulk RNA-seq data.
+#'
+#'
+#' @name rse_tx
+#' @docType data
+#' @format A [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class]
+#' @keywords datasets
+#' @seealso [getPCs] [k_qsvs] [getDegTx] [qSVA]
+NULL