select_transcripts: Select transcripts associated with degradation

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

Select transcripts associated with degradation

Description

Helper function to select which experimental model(s) will be used to generate the qSVs. Degradation-associated transcripts are derived in four different models (transcripts). The cell_component parameter controls whether the models with cell-type proportions are included. This function extract the top top_n transcripts found to be significant in each considered model, then returns the union of transcripts across all considered models. Up to 10,000 transcripts are available to select from each model prior to taking the union.

Usage

select_transcripts(top_n = 1000, cell_component = FALSE)

Arguments

top_n	An integer(1) specifying how many significant transcripts to extract from each model prior to taking a union across models.
cell_component	A logical(1). If FALSE, only include transcripts from the main and interaction models (see main_model and int_model here: transcripts). If TRUE, additionally include main and interaction models that include cell-type proportions (a total of 4 models).

Value

A character() with the transcript IDs.

Examples

## Default set of transcripts associated with degradation
sig_transcripts <- select_transcripts()
length(sig_transcripts)
head(sig_transcripts)

## Select more transcripts if desired
length(select_transcripts(top_n = 5000))

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