getDegTx: Obtain expression matrix for degraded transcripts

In LieberInstitute/qsvaR: Generate Quality Surrogate Variable Analysis for Degradation Correction

Obtain expression matrix for degraded transcripts

Description

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.

Usage

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

Value

A RangedSummarizedExperiment-class object.

Examples

degTx <- getDegTx(rse_tx)

LieberInstitute/qsvaR documentation built on Dec. 14, 2024, 10:30 p.m.