transcripts: Transcripts for Degradation Models

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

Transcripts for Degradation Models

Description

An object storing three lists of transcripts each corresponding to a model used in the degradation experiment. 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.

Usage

transcripts

Format

A list() with character strings containing the transcripts selected by each model. Each string is a GENCODE transcript IDs.

See Also

select_transcripts

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