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
)
A RangedSummarizedExperiment-class object containing the transcript data desired to be studied.
A character()
vector of transcripts that should be
associated with degradation, expected to be present in rownames(rse_tx)
.
character string specifying the name of the assay desired in rse_tx
specify if the function should report how many model transcripts were matched
A RangedSummarizedExperiment-class object.
degTx <- getDegTx(rse_tx)
#> Using 1044 degradation-associated transcripts.