This function is used to obtain a RangedSummarizedExperiment-class of transcripts and their expression values #' These transcripts are selected based on a prior study of RNA degradation in postmortem brain tissues. This object can later be used to obtain the principle components necessary to remove the effect of degradation in differential expression.

getDegTx(
  rse_tx,
  sig_transcripts = select_transcripts(),
  assayname = "tpm",
  verbose = TRUE
)

Arguments

rse_tx

A RangedSummarizedExperiment-class object containing the transcript data desired to be studied.

sig_transcripts

A character() vector of transcripts that should be associated with degradation, expected to be present in rownames(rse_tx).

assayname

character string specifying the name of the assay desired in rse_tx

verbose

specify if the function should report how many model transcripts were matched

Examples

degTx <- getDegTx(rse_tx)
#> Using 1044 degradation-associated transcripts.