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 will be used to generate the qSVs.

Usage

select_transcripts(type = c("cell_component", "top1500", "standard"))

Arguments

type

A character(1) specifying the transcripts set type. These were determined by Joshua M. Stolz et al, 2022. Here the names "cell_component", "top1500", and "standard" refer to models that were determined to be effective in removing degradation effects. The "standard" model involves taking the union of the top 1000 transcripts associated with degradation from the interaction model and the main effect model. The "top1500" model is the same as the "standard model except the union of the top 1500 genes associated with degradation is selected. The most effective of our models, "cell_component", involved deconvolution of the degradation matrix to determine the proportion of cell types within our studied tissue. These proportions were then added to our model.matrix() and the union of the top 1000 transcripts in the interaction model, the main effect model, and the cell proportions model were used to generate this model of qSVs.

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)

## Example where match.arg() auto-completes
select_transcripts("top")

LieberInstitute/qsvaR documentation built on June 22, 2024, 8:03 a.m.